Chaos and hyperchaos in simple gene network with negative feedback and time delays

2017 ◽  
Vol 15 (02) ◽  
pp. 1650042 ◽  
Author(s):  
Tamara M. Khlebodarova ◽  
Vladislav V. Kogai ◽  
Stanislav I. Fadeev ◽  
Vitaly A. Likhoshvai
Keyword(s):  
Gene Networks ◽  
Chaotic Dynamics ◽  
Gene Network ◽  
Point Of View ◽  
Evolutionary Selection ◽  
Delayed Argument ◽  
Regulatory Circuits ◽  
Emergence Of Chaos ◽  
Synthesis And Degradation

Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos. It has been shown that one of such circuits may be a combination of negative autoregulation of expression of transcription factors at the level of their synthesis and degradation. The presence of such a circuit results in formation of multiple branches of chaotic solutions as well as formation of hyperchaos with equal and sufficiently low values of the delayed argument that can be implemented not only in eukaryotic, but in prokaryotic cells.

A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks

2017 ◽  
Vol 15 (02) ◽  
pp. 1650045 ◽  
Author(s):  
Olga V. Petrovskaya ◽  
Evgeny D. Petrovskiy ◽  
Inna N. Lavrik ◽  
Vladimir A. Ivanisenko
Keyword(s):  
Mathematical Modeling ◽  
Gene Regulatory Networks ◽  
Gene Networks ◽  
Gene Network ◽  
Regulatory Networks ◽  
Network Modeling ◽  
Computer Experiments ◽  
Linear Control ◽  
Expression Of Genes ◽  
Gene Regulatory

Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts. Structural analysis of graphs of generated mosaic gene regulatory networks has revealed that the most important factor for building accurate integrated mathematical models, among those analyzed in the study, is data on expression of genes corresponding to the vertices with high properties of centrality.

scholarly journals On Robust State Estimation of Gene Networks

2010 ◽  
Vol 2 ◽  
pp. 117959721000200 ◽  
Author(s):  
Chia-Hua Chuang ◽  
Chun-Liang Lin
Keyword(s):  
Parameter Estimation ◽  
Kalman Filter ◽  
Quantitative Analysis ◽  
State Estimation ◽  
Gene Networks ◽  
Gene Network ◽  
Biological Systems ◽  
Uncertain Process ◽  
Network Systems ◽  
Internal States

Gene networks in biological systems are not only nonlinear but also stochastic due to noise corruption. How to accurately estimate the internal states of the noisy gene networks is an attractive issue to researchers. However, the internal states of biological systems are mostly inaccessible by direct measurement. This paper intends to develop a robust extended Kalman filter for state and parameter estimation of a class of gene network systems with uncertain process noises. Quantitative analysis of the estimation performance is conducted and some representative examples are provided for demonstration.

scholarly journals Synthesis and degradation rates of collagens in vivo in whole skin of rats, studied with 18O2 labelling

1986 ◽  
Vol 240 (2) ◽  
pp. 431-435 ◽  
Author(s):  
J A Molnar ◽  
N Alpert ◽  
J F Burke ◽  
V R Young
Keyword(s):  
Gas Chromatography Mass Spectrometry ◽  
Collagen Turnover ◽  
Growing Rats ◽  
Soluble Collagen ◽  
Insoluble Collagen ◽  
Degradation Rates ◽  
Labelling Procedure ◽  
Skin Biopsies ◽  
Synthesis And Degradation

Rats of synthesis and degradation in vivo of collagens in 0.5 M-acetic acid-soluble and -insoluble extracts from skins of three growing rats were determined by using a labelling procedure involving exposure of the animals to an atmosphere of 18O2 for 36 h. For comparison, rats also received injections of [2H]proline. Serial skin biopsies were taken at frequent intervals over 392 days. Enrichment of 18O and 2H in the hydroxyproline of the collagen fractions was determined by gas chromatography-mass spectrometry. Changes in size of the soluble and insoluble collagen pools were considered in the evaluation of isotope kinetic data. The insoluble collagen fraction showed no degradation. The efflux (mean +/- S.D., expressed as mumol of hydroxyproline) from the soluble collagen pool was estimated to be 59.9 +/- 1.9 per day from the 18O data, and 25.5 +/- 7.5 per day from the 2H results. The finding indicates significant reutilization of 2H-radiolabelled proline for hydroxyproline synthesis. From these isotope data and estimates of size of the collagen pools it was determined that 55% of the collagen disappearing from the soluble pool was due to maturation into insoluble collagens and 45% of the disappearance was a result of actual degradation of soluble collagen. These results confirm the utility of 18O2 as a non-reutilizable label for studies of collagen turnover in vivo.

scholarly journals From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis

2014 ◽  
Vol 369 (1657) ◽  
pp. 20130542 ◽  
Author(s):  
David-Emlyn Parfitt ◽  
Michael M. Shen
Keyword(s):  
Stem Cells ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Cell Lineage ◽  
Network Models ◽  
Cell Types ◽  
Mammalian Development ◽  
A Genome

To date, many regulatory genes and signalling events coordinating mammalian development from blastocyst to gastrulation stages have been identified by mutational analyses and reverse-genetic approaches, typically on a gene-by-gene basis. More recent studies have applied bioinformatic approaches to generate regulatory network models of gene interactions on a genome-wide scale. Such models have provided insights into the gene networks regulating pluripotency in embryonic and epiblast stem cells, as well as cell-lineage determination in vivo . Here, we review how regulatory networks constructed for different stem cell types relate to corresponding networks in vivo and provide insights into understanding the molecular regulation of the blastocyst–gastrula transition.

scholarly journals Regulatory links between imprinted genes: evolutionary predictions and consequences

2016 ◽  
Vol 283 (1824) ◽  
pp. 20152760 ◽  
Author(s):  
Manus M. Patten ◽  
Michael Cowley ◽  
Rebecca J. Oakey ◽  
Robert Feil
Keyword(s):  
Gene Networks ◽  
Cellular Proliferation ◽  
Point Of View ◽  
Imprinted Genes ◽  
Imprinted Gene ◽  
Genome Wide ◽  
Proliferation And Differentiation ◽  
Evolutionary View ◽  
In Trans ◽  
Regulatory Effects

Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis -acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans -regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.

scholarly journals Independent Recruitment of Mediator and SAGA by the Activator Met4

2006 ◽  
Vol 26 (8) ◽  
pp. 3149-3163 ◽  
Author(s):  
Christophe Leroy ◽  
Laëtitia Cormier ◽  
Laurent Kuras
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Rna Polymerase Ii ◽  
Gene Network ◽  
Pol Ii ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Target Promoters ◽  
Sulfur Containing

ABSTRACT Mediator is a key RNA polymerase II (Pol II) cofactor in the regulation of eukaryotic gene expression. It is believed to function as a coactivator linking gene-specific activators to the basal Pol II initiation machinery. In support of this model, we provide evidence that Mediator serves in vivo as a coactivator for the yeast activator Met4, which controls the gene network responsible for the biosynthesis of sulfur-containing amino acids and S-adenosylmethionine. In addition, we show that SAGA (Spt-Ada-Gcn5-acetyltransferase) is also recruited to Met4 target promoters, where it participates in the recruitment of Pol II by a mechanism involving histone acetylation. Interestingly, we find that SAGA is not required for Mediator recruitment by Met4 and vice versa. Our results provide a novel example of functional interplay between Mediator and coactivators involved in histone modification.

A NEW METHOD OF DETERMINING THRESHOLD OF GENE NETWORK BASED ON PHENOTYPES

2011 ◽  
Vol 19 (04) ◽  
pp. 607-616
Author(s):  
YUANYUAN ZHANG ◽  
SHUDONG WANG ◽  
MEIXI YANG ◽  
DASHUN XU ◽  
DAZHI MENG
Keyword(s):  
Gene Networks ◽  
Gene Network ◽  
Structural Parameters ◽  
Network Modeling ◽  
Genetic Diseases ◽  
Disease Stage ◽  
External Representation ◽  
Functional Relationships ◽  
Disease Phenotypes ◽  
Significant Difference

With the rapid growth of microarray data, it has become a hot topic to reveal complex behaviors and functions of life system by studying the relationships among genes. In the process of reverse network modeling, the relationships with less relevance are generally not considered by determining a threshold when the relationships among genes are mined. However, there are no effective methods to determine the threshold up to now. It is worthwhile to note that the phenotypes of genetic diseases are generally regarded as external representation of the functions of genes. Therefore, two types of phenotype networks are constructed from gene and disease views, respectively, and through comparing these two types of phenotype networks, the threshold of gene network corresponding to a certain disease can be determined when their similarity reaches to maximum. Because the gene network is determined based on the relationships among phenotypes and phenotypes are external representation of the functions of genes, it is considered that relationships in the gene network may show functional relationships among genes in biological system. In this work, the thresholds 0.47 and 0.48 of gene network are determined based on Parkinson disease phenotypes. Furthermore, the validity of these thresholds is verified by the specificity and susceptibility of phenotype networks. Also, through comparing the structural parameters of gene networks for normal and disease stage at different thresholds, significant difference between the two gene networks at threshold 0.47 or 0.48 is found. The significant difference of structural parameters further verifies the efficiency of this method.

scholarly journals Age-related changes in collagen synthesis and degradation in rat tissues. Importance of degradation of newly synthesized collagen in regulating collagen production

1991 ◽  
Vol 276 (2) ◽  
pp. 307-313 ◽  
Author(s):  
P K Mays ◽  
R J McAnulty ◽  
J S Campa ◽  
G J Laurent
Keyword(s):  
Skeletal Muscle ◽  
Collagen Synthesis ◽  
Rat Tissues ◽  
Age Related ◽  
Developmental Growth ◽  
Cross Links ◽  
Fractional Synthesis ◽  
Synthesis And Degradation ◽  
Age Related Changes

During developmental growth, collagens are believed to be continuously deposited into an extracellular matrix which is increasingly stabilized by the formation of covalent cross-links throughout life. However, the age-related changes in rates of synthetic and degradative processes are less well understood. In the present study we measured rates of collagen synthesis in vivo using a flooding dose of unlabelled proline given with [14C]proline and determining production of hydroxy[14C]proline. Degradation of newly synthesized collagen was estimated from the amount of free hydroxy [14C]proline in tissues 30 min after injection. Collagen fractional synthesis rates ranged from about 5%/day in skeletal muscle to 20%/day in hearts of rats aged 1 month. At 15 months of age, collagen fractional synthesis rates had decreased markedly in lung and skin, but in skeletal muscle and heart, rates were unchanged. At 24 months of age, synthesis rates had decreased by at least 10-fold in all tissues, compared with rates at 1 month. The proportion of newly synthesized collagen degraded ranged from 6.4 +/- 0.4% in skin to 61.6 +/- 5.0% in heart at 1 month of age. During aging the proportion degraded increased in all tissues to maximal values at 15 months, ranging from 56 +/- 7% in skin to 96 +/- 1% in heart. These data suggest that there are marked age-related changes in rates of collagen metabolism. They also indicate that synthesis is active even in old animals, where the bulk of collagens produced are destined to be degraded.

scholarly journals “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network

2018 ◽  
Vol 115 (32) ◽  
pp. E7615-E7623 ◽  
Author(s):  
Florencia Garrido-Charad ◽  
Tomas Vega-Zuniga ◽  
Cristián Gutiérrez-Ibáñez ◽  
Pedro Fernandez ◽  
Luciana López-Jury ◽  
...  
Keyword(s):  
Point Of View ◽  
Stimulus Selection ◽  
Common Input ◽  
Computational Point ◽  
Specific Subset ◽  
Neural Processes ◽  
Neural Tracing ◽  
Input Signals

The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity.

scholarly journals Between biology and medicine: perspectives on the use of dendritic cells in anticancer therapy

2017 ◽  
Vol 71 (0) ◽  
pp. 0-0
Author(s):  
Agnieszka Szczygieł ◽  
Elżbieta Pajtasz-Piasecka
Keyword(s):  
Dendritic Cells ◽  
Ex Vivo ◽  
Anticancer Therapy ◽  
Point Of View ◽  
Proper Function ◽  
Innate And Adaptive Immunity ◽  
Factors Affecting ◽  
Antigen Presenting

Dendritic cells (DCs), as a link between innate and adaptive immunity, play a pivotal role in maintaining homeostasis of the immune system. The DC population is characterized by heterogeneity; it consists of many subpopulations which, despite their phenotypic and localization differences, play an essential function – they are professional antigen presenting cells. Due to their role, DCs can be utilized in a new cancer treatment strategy. Their main purpose is to generate an anticancer response leading to the elimination of cancer cells. The tumor microenvironment, abundant in immunosuppressive factors (e.g. IL-10, TGF-β, Arg1, IDO), impairs the proper function of DCs. For this reason, various strategies are necessary for ex vivo preparation of DC-based vaccines and for the support of in vivo DCs to fight against tumors. DC-based vaccines are combined with other forms of immunotherapy (e.g. blockade of immune checkpoint molecules, e.g. PD-1 or CTLA-4) or conventional types of therapies (e.g. chemotherapy). Despite the enormous progress that has been made in anticancer therapy in the past two decades, there are still many unresolved issues regarding the effectiveness of the DCs usage. In this paper we described, in both a mouse and a human subject, a series of DC subpopulations, differentiating in normal conditions or under the influence of cancer microenvironment. We listed factors affecting the quality of the in vivo and ex vivo generations of antitumoral responses, significant from a therapeutic point of view. Moreover, the most important strategies for the use of DCs in anticancer therapies, as well as further developments on this field, have been discussed.

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