Genetic Regulatory Pathways Research Articles

Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.

Differential Dynamic Properties of Scleroderma Fibroblasts in Response to Perturbation of Environmental Stimuli

Diseases are believed to arise from dysregulation of biological systems (pathways) perturbed by environmental triggers. Biological systems as a whole are not just the sum of their components, rather ever-changing, complex and dynamic systems over time in response to internal and external perturbation. In the past, biologists have mainly focused on studying either functions of isolated genes or steady-states of small biological pathways. However, it is systems dynamics that play an essential role in giving rise to cellular function/dysfunction which cause diseases, such as growth, differentiation, division and apoptosis. Biological phenomena of the entire organism are not only determined by steady-state characteristics of the biological systems, but also by intrinsic dynamic properties of biological systems, including stability, transient-response, and controllability, which determine how the systems maintain their functions and performance under a broad range of random internal and external perturbations. As a proof of principle, we examine signal transduction pathways and genetic regulatory pathways as biological systems. We employ widely used state-space equations in systems science to model biological systems, and use expectation-maximization (EM) algorithms and Kalman filter to estimate the parameters in the models. We apply the developed state-space models to human fibroblasts obtained from the autoimmune fibrosing disease, scleroderma, and then perform dynamic analysis of partial TGF-β pathway in both normal and scleroderma fibroblasts stimulated by silica. We find that TGF-β pathway under perturbation of silica shows significant differences in dynamic properties between normal and scleroderma fibroblasts. Our findings may open a new avenue in exploring the functions of cells and mechanism operative in disease development.

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

Pax2 expression patterns in the developing chick inner ear

The fate specification of the developing vertebrate inner ear could be determined by complex regulatory genetic pathways involving the Pax2/5/8 genes. Pax2 expression has been reported in the otic placode and vesicle of all vertebrates that have been studied. Loss-of-function experiments suggest that the Pax2 gene plays a key role in the development of the cochlear duct and acoustic ganglion. Despite all these data, the role of Pax2 gene in the specification of the otic epithelium is still only poorly defined. In the present work, we report a detailed study of the spatial and temporal Pax2 expression patterns during the development of the chick inner ear. In the period analysed, Pax2 is expressed only in some presumptive sensory patches, but not all, even though all sensory patches show the scattered Pax2 expression pattern later on. We also show that Pax2 is also expressed in several non-sensory structures.

Quantitative inference of dynamic regulatory pathways via microarray data

BackgroundThe cellular signaling pathway (network) is one of the main topics of organismic investigations. The intracellular interactions between genes in a signaling pathway are considered as the foundation of functional genomics. Thus, what genes and how much they influence each other through transcriptional binding or physical interactions are essential problems. Under the synchronous measures of gene expression via a microarray chip, an amount of dynamic information is embedded and remains to be discovered. Using a systematically dynamic modeling approach, we explore the causal relationship among genes in cellular signaling pathways from the system biology approach.ResultsIn this study, a second-order dynamic model is developed to describe the regulatory mechanism of a target gene from the upstream causality point of view. From the expression profile and dynamic model of a target gene, we can estimate its upstream regulatory function. According to this upstream regulatory function, we would deduce the upstream regulatory genes with their regulatory abilities and activation delays, and then link up a regulatory pathway. Iteratively, these regulatory genes are considered as target genes to trace back their upstream regulatory genes. Then we could construct the regulatory pathway (or network) to the genome wide. In short, we can infer the genetic regulatory pathways from gene-expression profiles quantitatively, which can confirm some doubted paths or seek some unknown paths in a regulatory pathway (network). Finally, the proposed approach is validated by randomly reshuffling the time order of microarray data.ConclusionWe focus our algorithm on the inference of regulatory abilities of the identified causal genes, and how much delay before they regulate the downstream genes. With this information, a regulatory pathway would be built up using microarray data. In the present study, two signaling pathways, i.e. circadian regulatory pathway in Arabidopsis thaliana and metabolic shift pathway from fermentation to respiration in yeast Saccharomyces cerevisiae, are reconstructed using microarray data to evaluate the performance of our proposed method. In the circadian regulatory pathway, we identified mainly the interactions between the biological clock and the photoperiodic genes consistent with the known regulatory mechanisms. We also discovered the now less-known regulations between crytochrome and phytochrome. In the metabolic shift pathway, the casual relationship of enzymatic genes could be detected properly.

Intronic microRNAs

MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular mRNAs that contain partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. MiRNA was originally discovered in the intergenic regions of the Caenorhabditis elegans genome as native RNA fragments that modulate a wide range of genetic regulatory pathways during animal development. However, neither RNA promoter nor polymerase responsible for miRNA biogenesis was determined. Recent findings of intron-derived miRNA in C. elegans, mouse, and human have inevitably led to an alternative pathway for miRNA biogenesis, which relies on the coupled interaction of Pol-II-mediated pre-mRNA transcription and intron excision, occurring in certain nuclear regions proximal to genomic perichromatin fibrils.

Gene expression networks underlying retinoic acid-induced differentiation of human retinoblastoma cells.

To understand the genetic regulatory pathways underlying the retinoic acid (RA) induction of cone arrestin, gene array technology and other molecular tools were used to profile global gene expression changes in human retinoblastoma cells. Weri-Rb-1 retinoblastoma cells were cultured in the absence or presence of RA for various periods. DNA microarray analysis profiled gene expression followed by real-time PCR and Northern and immunoblot analyses to confirm the change in expression of selected retinal genes and their gene products. Additional methodology included flow cytometry analysis, immunocytochemistry, and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay. DNA microarray analysis of approximately 6800 genes revealed RA-induced upregulation of cone-specific genes and downregulation of rod-specific genes in Weri-Rb-1 cells. Other significantly upregulated mRNAs included chicken ovalbumin upstream promoter-transcription factor (COUP-TF1), retinoid X receptor (RXR)-gamma, thyroid hormone receptor (TR)-beta2, and guanylyl cyclase-activating protein (GCAP)-1. Real-time PCR and/or Northern blot analysis confirmed the expression changes of a subset of genes including the upregulation of a pineal- and retina-specific transcription factor, CRX. RA treatment also led to G(0)/G(1) cell cycle arrest and increased both the intensity of human cone arrestin (hCAR)-immunoreactivity and the number of apoptotic cells. The cell-cycle-arrest stage correlated with the observed microarray results in which the RA treatment downregulated critical genes such as cyclins (cyclin E, cyclin D3) and cyclin-dependent kinases (CDK5, CDK10). These data suggest that RA induces a subpopulation of retinoblastoma cells to differentiate toward a cone cell lineage while selectively leading other cells into apoptosis.

Rapid Speciation via Parallel, Directional Selection on Regulatory Genetic Pathways

Regulatory genetic pathways are ubiquitous in organisms and play a central role in the realization of the phenotype during development. We explored the proposition that these pathways can provide a plausible source of the epistatic variation that has been implicated in the evolution of postzygotic reproductive isolation. We modeled gene regulation as a matching function between the product of one locus and the promoter site of the next locus in the pathway, with binding strength determining the amount of product. When the phenotype is subject to parallel selection in a pair of independent populations, we find that the fitnesses of F1and F2hybrids often drop to very low values as the populations respond in genetically different and incompatible ways. The simulations support the predictions of the analytical models. Hybrid fitness reduction occurs more often as the number of loci in the pathway increases, and as the binding site interactions become more complex. Less hybrid fitness reduction is seen when the populations start with imperfect binding in the pathway. In contrast, when we constructed the phenotype without gene regulation using multiplicative rules, isomorphic to the additive phenotype commonly assumed in evolutionary models, we found no appreciable F1fitness reduction and only slight F2fitness reduction. The interaction of genetic drift and mutation, even at very high rates, did not reduce hybrid fitness at all on the time-scales we considered. Clearly, the evolution of regulatory genetic pathways can play an important role in speciation, but much more empirical information is needed on the effect of allelic variability in regulatory site interactions before this role is fully understood.

The development of granulomas in schistosomiasis: genetic backgrounds, regulatory pathways, and specific egg antigen responses that influence the magnitude of disease

This paper describes the immunophenotype of cellular inflammatory infiltrates in chronic cholangitis in six common dolphins (Delphinus delphis), four striped dolphins (Stenella coeruleoalba), three Atlantic spotted dolphins (Stenella frontalis) and one pygmy sperm whale (Kogia Breviceps) found stranded along the coasts of the Canary Islands (Spain). A panel of 5 antibodies previously tested in dolphins (anti-CD3, -IgG, -MHC class II, -S100 protein and -lysozyme) were used. The present work also reports cross reactivity with dolphin antigens of two antibodies not used to date in dolphins (anti-mouse iNOS and anti-mouse Foxp3). The most common type of cholangitis found was chronic granulomatous cholangitis, associated with the presence of the parasite Campula spp., or its eggs in bile ducts. The cellular composition of the hepatic inflammatory infiltrate associated to chronic parasitic cholangitis was closely similar to that found in the cortex of control lymph nodes, including the presence of S100+ and MHC class II+ dendritic-like cells in lymphoid follicles and interfollicular areas. Only occasional macrophages expressed iNOS, whereas Foxp3+ lymphocytes were not found in any of the lesions described in the different types of cholangitis.

Catalytic Mechanism and Specificity for Hydrolysis and Transglycosylation Reactions of Cytosolic β-Glucosidase from Guinea Pig Liver

Cytosolic beta-glucosidase (CBG) from mammalian liver is known for its broad substrate specificity and has been implicated in the transformation of xenobiotic glycosides. CBG also catalyzes a variety of transglycosylation reactions, which have been been shown with other glycosylhydrolases to function in synthetic and genetic regulatory pathways. We investigated the catalytic mechanism, substrate specificity, and transglycosylation acceptor specificity of guinea pig liver CBG by several methods. These studies indicate that CBG employs a two-step catalytic mechanism with the formation of a covalent enzyme-sugar intermediate and that CBG will transfer sugar residues to primary hydroxyls and equatorial but not axial C-4 hydroxyls of aldopyranosyl sugars. Kinetic studies revealed that correction for transglycosylation reactions is necessary to derive correct kinetic parameters for CBG. Further analyses revealed that for aldopyranosyl substrates, the activation energy barrier is affected most by the presence of a C-6 carbon and by the configuration of the C-2 hydroxyl, whereas the binding energy is affected modestly by the configuration and substituents at C-2, C-4, and C-5. These data indicate that the transglycosylation activity of CBG derives from the formation of a covalently linked enzyme-sugar intermediate and that the specificity of CBG for transglycosylation reactions is different from its specificity for hydrolysis reactions.

Role of the heat-shock response in the life and death of proteins.

Changes in protein levels and the folded states of proteins are sensed by molecular chaperones and the degradative machinery that function to maintain cellular protein homeostasis. The importance of these systems is highlighted by their high degree of functional and structural conservation across evolution, from prokaryotes to eukaryotes, and their essential roles in a variety of cellular functions. The chaperone network, proteases, and components of the degradative machinery are also linked by common genetic regulatory pathways. For example, many of the proteins involved in protein folding and degradation are also heat-shock proteins whose expression is induced when cells are stressed and accumulate denatured or malfolded proteins. The family of heat-shock proteins (HSPs) encompasses a number of functionally related proteins that are expressed constitutively and/or at elevated levels upon exposure of cells to a variety of stress conditions including elevated temperature, arsenite, heavy metals, amino acid analogues, and oxidants. The chaperones and proteolytic systems often function together to determine the ultimate fates of proteins and are often coordinately regulated, as outlined in FIGURE 1. The heat-shock response regulates proteolysis by enhancing the expression of proteolytic factors and proteases, as well as of chaperones which may function as cofactors for proteolysis. The stress response in both prokaryotes and eukaryotes is, in turn, regulated by the proteolytic machinery (also A. Mathew, S. K. Mathur, and R. I. Morimoto, unpublished observations). This review will address the chaperone requirements in eukaryotic proteolysis and the regulation of eukaryotic chaperone expression by the ubiquitin–proteasome proteolytic system. A number of recent reviews have also addressed chaperone activities associated with proteolysis in prokaryotes and eukaryotes.

Chemical inhibition of epibiota by Australian seaweeds

Detailed, ecologically realistic studies of chemical inhibition of fouling (epibiosis) by marine organisms are rare. A first step in understanding chemical mediation of the interaction between epibionts and their hosts is to quantify potential inhibitory molecules on or near the surface of an alga (or other organisms) in the field. In situ quantification can be difficult, and measurements will be affected by the polarity of the molecules, hydrodynamics, ultrastructure of the producing organism, and the specific chemical structure of the molecules. All these factors also influence the effects of the compounds on epibiota. Here, some approaches are described to address these issues, emphasizing the need for ecological realism in measuring active ingredients, testing against ecologically relevant epibiota, and conducting, whenever possible, experiments and measurements in the field. Evidence to date indicates that active natural inhibitors of colonization are mostly non‐polar metabolites. However, not all non‐polar metabolites appear to be effective at inhibiting epibiota, either because the compounds are not presented at or near the surface of the host organisms in an appropriate way, or because they have low activity against relevant fouling organisms. This variation in the activity of different non‐polar metabolites appears to be primarily due to differences in their effect as chemicals per se rather than differences in their physicochemical properties, although in most instances the specific physiological mechanisms by which metabolites inhibit fouling organisms are not known. However, for halogenated furanones from Delisea pulchra, current research suggests that these metabolites inhibit bacterial colonization of the host alga by interfering with a class of bacterial genetic regulatory pathways known as AHL (acylated homoserine lactone) regulatory systems.

Selected Aspects of Homeobox Gene Function during Mammalian Development.

The genetic pathways of development are only beginning to be revealed. But the tools now exist to allow the rapid isolation of genes that carry sequence motifs such as the homeobox, zinc finger or basic-helix loop helix that can mark genes of special developmental significance. Expression patterns are readily determined by in situ hybridization and in vivo developmental functions can be analyzed by generating mice with targeted mutations. Upstream regulators of genes can be identified by finding proteins that bind to cis-regulatory elements. Downstream targets are more difficult to find but there are polymerase chain reaction approaches to define sequences bound by transcription factors and subtractive library approaches to finding specific targets. Although an enormous amount of work remains to be done it is clear that the basic techniques necessary to understand the genetic program of mammalian development are now available. As these techniques are applied and refined we will elaborate the genetic regulatory pathways of organogenesis. This will be deeply satisfying from an intellectual perspective. It will also lead to a better understanding of birth defects and to better treatments of a variety of diseases that involve organ malformation or deterioration. Copyright 1994 S. Karger AG, Basel