A statistical mechanics model for the collective epigenetic histone modification dynamics

2014 ◽  
Author(s):  
Hang Zhang ◽  
XIAO-JUN TIAN ◽  
Abhishek Mukhopadhyay ◽  
Kenneth S Kim ◽  
Jianhua Xing
Keyword(s):  
Histone Modifications ◽  
Nearest Neighbor ◽  
Covalent Modification ◽  
Type Model ◽  
Theoretical Studies ◽  
Lateral Interactions ◽  
Epigenetic Memory ◽  
Cellular Processes ◽  
Mechanics Model ◽  
Cell Phenotypes

Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a Potts-type model based on experimentally observed nearest-neighbor enzyme lateral interactions and nucleosome covalent modification state biased enzyme recruitment. The model can lead to effective nonlocal interactions among nucleosomes suggested in previous theoretical studies, and epigenetic memory is robustly inheritable against stochastic cellular processes.

Suspended animation: the molecular basis of metabolic depression

1988 ◽  
Vol 66 (1) ◽  
pp. 124-132 ◽  
Author(s):  
Kenneth B. Storey
Keyword(s):  
Metabolic Rate ◽  
Molecular Mechanisms ◽  
Complete Information ◽  
Covalent Modification ◽  
Metabolic Depression ◽  
Low Oxygen ◽  
Cellular Processes ◽  
Regulatory Enzymes ◽  
Hypometabolic State ◽  
Glycolytic Rate

An impressive array of organisms is capable of radically depressing basal metabolic rate and entering a hypometabolic state characterized by a marked reduction of many normal physiological functions. Environmental cues are often the trigger: low oxygen, low temperature, or lack of water, for example. Entry into a hypometabolic state does not, apparently, involve major biochemical reorganization but appears, instead, to result from molecular controls operating at a level "above" that of allosteric regulation of enzymes and "below" that of gene expression. The mechanisms involved are widely applicable to the coordinated inactivation of many cellular processes. Studies of anaerobiosis in marine molluscs provide the most complete information on the molecular mechanisms involved in metabolic rate depression. Glycolytic rate depression in the marine whelk involves (i) covalent modification of key regulatory enzymes (e.g., phosphofructokinase, pyruvate kinase) via enzyme phosphorylation to produce less active enzyme forms, (ii) dissociation of enzymes from complexes bound to the subcellular particulate fraction to disrupt pathway flux, and (iii) decreased levels of fructose-2,6-bisphosphate, a potent activator of phosphofructokinase, to help limit the anabolic uses of carbohydrate in the depressed state. Continuing studies are demonstrating the universality of these mechanisms as the basis of metabolic depression, including involvement in mammalian hibernation and anoxia tolerance in goldfish and turtles.

scholarly journals Observation of Antichiral Edge States in a Circuit Lattice

2020 ◽  
Author(s):  
Yuting Yang ◽  
Dejun Zhu ◽  
Zhi Hong Hang ◽  
Yidong Chong
Keyword(s):  
Nearest Neighbor ◽  
Electrical Circuit ◽  
Theoretical Studies ◽  
Magnetic Vector Potential ◽  
Edge States ◽  
Magnetic Vector ◽  
Haldane Model ◽  
Unusual Phenomenon ◽  
Key Features ◽  
Group Velocities

Abstract We constructed an electrical circuit to realize a modified Haldane lattice exhibiting the unusual phenomenon of antichiral edge states. The circuit consists of a network of inductors and capacitors with interconnections reproducing the effects of a magnetic vector potential. The next nearest neighbor hoppings are configured differently from the standard Haldane model, and as predicted by earlier theoretical studies, this gives rise to antichiral edge states that propagate in the same direction on opposite edges and co-exist with bulk states at the same frequency. Using pickup coils to measure the voltage distributions in the circuit, we experimentally verify the key features of the modified Haldane lattice, including the group velocities of the antichiral edge states.

Optimal Determination of Respiratory Airflow Patterns for a General Multicompartment Lung Mechanics System With Nonlinear Resistance and Compliance Parameters

2015 ◽  
Vol 137 (12) ◽  
Author(s):  
Saing Paul Hou ◽  
Nader Meskin ◽  
Wassim M. Haddad
Keyword(s):  
Optimization Criterion ◽  
Lung Model ◽  
Lung Mechanics ◽  
Type Model ◽  
Airflow Rate ◽  
Mechanics Model ◽  
Respiratory Airflow ◽  
Elastic Potential Energy ◽  
And Function ◽  
Nonlinear Resistance

In this paper, we develop a framework for determining optimal respiratory airflow patterns for a multicompartment lung mechanics system with nonlinear resistance and compliance parameters. First, a nonlinear multicompartment lung mechanics model that accounts for nonlinearities in both the airway resistances and the lung compliances is developed. In particular, we assume that the resistive losses are characterized by a Rohrer-type model with resistive losses defined as the sum of linear and quadratic terms of the airflow. The proposed model is more realistic than those presented in the literature, since it takes into account the heterogeneity of lung anatomy and function as well as the nonlinearity of lung resistance and compliance parameters. This model can be used to provide a better understanding of pulmonary function as well as the process of mechanical ventilation. Next, using the proposed nonlinear multicompartment lung model, we develop a framework for determining optimal respiratory airflow patterns. Specifically, an optimization criterion that involves the minimization of the oxygen consumption of the lung muscles and lung volume acceleration for the inspiratory phase, and the minimization of the elastic potential energy and rapid airflow rate changes for the expiratory phase is formulated and solved. The solution to the formulated optimization problem is derived using classical calculus of variation techniques. Finally, several illustrative numerical examples are presented to illustrate the efficacy of the proposed nonlinear multicompartment lung model and the corresponding optimal airflow patterns. Comparison with experimental data shows that our nonlinear resistance model predicts the airflow patterns more accurately than linear resistance models. Moreover, the optimization criterion used in this paper also provides a more accurate prediction of the optimal airflow patterns.

scholarly journals Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals

2016 ◽  
Vol 63 (6) ◽  
pp. 1066-1079 ◽  
Author(s):  
Hui Zheng ◽  
Bo Huang ◽  
Bingjie Zhang ◽  
Yunlong Xiang ◽  
Zhenhai Du ◽  
...  
Keyword(s):  
Histone Modifications ◽  
Epigenetic Memory

scholarly journals Epigenetic Memory Independent of Symmetric Histone Inheritance

2019 ◽  
Author(s):  
Daniel S Saxton ◽  
Jasper Rine
Keyword(s):  
Gene Regulation ◽  
Dna Replication ◽  
Gene Silencing ◽  
Histone Modifications ◽  
Epigenetic Memory ◽  
Important Form

AbstractHeterochromatic gene silencing is an important form of gene regulation that usually requires specific histone modifications. A popular model posits that inheritance of modified histones, especially in the form of H3-H4 tetramers, underlies inheritance of heterochromatin. Because H3-H4 tetramers are randomly distributed between daughter chromatids during DNA replication, rare occurrences of asymmetric tetramer inheritance within a heterochromatic domain would have the potential to destabilize heterochromatin. This model makes a prediction that shorter heterochromatic domains would experience unbalanced tetramer inheritance more frequently, and thereby be less stable. In contrast to this prediction, we found that shortening a heterochromatic domain in Saccharomyces had no impact on the strength of silencing nor its heritability. Additionally, we found that replisome mutations that disrupt inheritance of H3-H4 tetramers had only minor effects on heterochromatin stability. These findings suggest that histones carry little or no memory of the heterochromatin state through DNA replication.

scholarly journals Phenotypic Variability of Bacterial Cell Cycle: Mathematical Model

2016 ◽  
Vol 11 (1) ◽  
pp. 91-113 ◽  
Author(s):  
В.А. Лихошвай ◽  
V.A. Likhoshvai
Keyword(s):  
Cell Cycle ◽  
Bacterial Cell ◽  
Phenotypic Variability ◽  
Molecular Genetic ◽  
Translation System ◽  
Enzymatic Reactions ◽  
Control Mechanisms ◽  
Cellular Processes ◽  
Bacterial Cell Cycle ◽  
Cell Phenotypes

The results of the study of mechanisms of different cell phenotypes occurrence in a genetically homogenous population using the bacterial cell cycle model are presented. It was shown that phenotypic variability represents an internal, immanent property of bacteria. The basis of this phenomenon is universal non-linear properties of the conjugated transcription-translation system, that controls all cellular processes. Phenotypic variability occurs in a simple, deterministic, self-reproducing system under the uniform transmission of the structural components to the daughter cells during division and in the absence of any special control mechanisms of molecular-genetic processes and enzymatic reactions.

A methodology for carbamate post-translational modification discovery and its application in Escherichia coli

2021 ◽  
Vol 11 (2) ◽  
pp. 20200028
Author(s):  
Victoria L. Linthwaite ◽  
Martin J. Cann
Keyword(s):  
Escherichia Coli ◽  
Carbon Dioxide ◽  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Signalling Pathways ◽  
Post Translational Modification ◽  
Cellular Targets ◽  
Biologically Relevant ◽  
Cellular Processes ◽  
Cell Phenotypes

Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO 2 regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO 2 interactions with diverse cellular targets. CO 2 is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by the model plant species Arabidopsis thaliana . Here, we describe a detailed methodology for identifying new carbamate PTMs in an extracted soluble proteome under biologically relevant conditions. We apply this methodology to the soluble proteome of the model prokaryote Escherichia coli and identify new carbamate PTMs . The application of this methodology, therefore, supports the hypothesis that the carbamate PTM is both more widespread in biology than previously suspected and may represent a broadly relevant mechanism for CO 2 –protein interactions.

scholarly journals Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation

2015 ◽  
Vol 36 (4) ◽  
pp. 615-627 ◽  
Author(s):  
Rodrigo A. Grandy ◽  
Troy W. Whitfield ◽  
Hai Wu ◽  
Mark P. Fitzgerald ◽  
Jennifer J. VanOudenhove ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Histone Modifications ◽  
Molecular Mechanisms ◽  
Embryonic Stem ◽  
Gene Promoters ◽  
Transition Analysis ◽  
Differentiated Cells ◽  
A Cell ◽  
Cycle Dependent ◽  
Cell Phenotypes

Stem cell phenotypes are reflected by posttranslational histone modifications, and this chromatin-related memory must be mitotically inherited to maintain cell identity through proliferative expansion. In human embryonic stem cells (hESCs), bivalent genes with both activating (H3K4me3) and repressive (H3K27me3) histone modifications are essential to sustain pluripotency. Yet, the molecular mechanisms by which this epigenetic landscape is transferred to progeny cells remain to be established. By mapping genomic enrichment of H3K4me3/H3K27me3 in pure populations of hESCs in G2, mitotic, and G1phases of the cell cycle, we found striking variations in the levels of H3K4me3 through the G2-M-G1transition. Analysis of a representative set of bivalent genes revealed that chromatin modifiers involved in H3K4 methylation/demethylation are recruited to bivalent gene promoters in a cell cycle-dependent fashion. Interestingly, bivalent genes enriched with H3K4me3 exclusively during mitosis undergo the strongest upregulation after induction of differentiation. Furthermore, the histone modification signature of genes that remain bivalent in differentiated cells resolves into a cell cycle-independent pattern after lineage commitment. These results establish a new dimension of chromatin regulation important in the maintenance of pluripotency.

Discrimination of membrane transporter protein types using K-nearest neighbor method derived from the similarity distance of total diversity measure

2015 ◽  
Vol 11 (3) ◽  
pp. 950-957 ◽  
Author(s):  
Yong-Chun Zuo ◽  
Wen-Xia Su ◽  
Shi-Hua Zhang ◽  
Shan-Shan Wang ◽  
Cheng-Yan Wu ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Membrane Transporters ◽  
Membrane Transporter ◽  
K Nearest Neighbor ◽  
Transporter Protein ◽  
Cellular Processes ◽  
Diversity Measure ◽  
Living Organisms ◽  
Similarity Distance ◽  
Total Diversity

Membrane transporters play crucial roles in the fundamental cellular processes of living organisms.

scholarly journals Single-cell and neuronal network alterations in an in vitro model of Fragile X syndrome

2018 ◽  
Author(s):  
Anastasiya Moskalyuk ◽  
R. Frank Kooy ◽  
Michele Giugliano
Keyword(s):  
Single Cell ◽  
Ex Vivo ◽  
Fragile X ◽  
Network Development ◽  
Cellular Processes ◽  
Wide Range ◽  
Clinical Consequences ◽  
Vitro Model ◽  
Cell Phenotypes

AbstractThe Fragile X mental retardation protein (FMRP) is involved in many cellular processes and it regulates synaptic and network development in neurons. Its absence is known to lead to intellectual disability, with a wide range of co-morbidities including autism. Over the past decades, FMRP research focused on abnormalities both in glutamatergic and GABAergic signalling, and an altered balance between excitation and inhibition has been hypothesised to underlie the clinical consequences of absence of the protein. Using FMRP knockout mice, we studied an in vitro model of cortical microcircuitry and observed that the loss of FMRP largely affected the electrophysiological correlates of network development and maturation but caused less alterations in single-cell phenotypes. Using a mathematical model, we demonstrated that the combination of an increased excitation and reduced inhibition describes best predicts our experimental observations during the ex vivo formation of the network connections.

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