A New Approach to Bioprocess Control by the Analysis of Regulatory Networks

1997 ◽  
Vol 30 (5) ◽  
pp. 197-202
Author(s):  
Karl Bayer ◽  
Monika Cserjan ◽  
Eberhard Dürrschmid
Keyword(s):  
Regulatory Networks ◽  
New Approach ◽  
Bioprocess Control

scholarly journals Balance equations can buffer noisy and sustained environmental perturbations of circadian clocks

2010 ◽  
Vol 1 (1) ◽  
pp. 177-186 ◽  
Author(s):  
Mirela Domijan ◽  
David A. Rand
Keyword(s):  
Temperature Compensation ◽  
Regulatory Networks ◽  
Circadian Clocks ◽  
Balance Equations ◽  
New Approach ◽  
Environmental Perturbations ◽  
Environmental Fluctuations ◽  
Free Running ◽  
Temperature Levels

We present a new approach to understanding how regulatory networks such as circadian clocks might evolve robustness to environmental fluctuations. The approach is in terms of new balance equations that we derive. We use it to describe how an entrained clock can buffer the effects of daily fluctuations in light and temperature levels. We also use it to study a different approach to temperature compensation where instead of considering a free-running clock, we study temperature buffering of the phases in a light-entrained clock, which we believe is a more physiological setting.

scholarly journals An ASP-based Approach for Boolean Networks Representation and Attractor Detection

10.29007/fb4f ◽  
2020 ◽  
Author(s):  
Tarek Khaled ◽  
Belaid Benhamou
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Answer Set Programming ◽  
Boolean Networks ◽  
Stable States ◽  
New Approach ◽  
Significant Step ◽  
The Subject ◽  
Gene Regulatory ◽  
Critical Aspects

In biology, Boolean networks are conventionally used to represent and simulate gene regulatory networks. The attractors are the subject of special attention in analyzing the dynamics of a Boolean network. They correspond to stable states and stable cycles, which play a crucial role in biological systems. In this work, we study a new representation of the dynamics of Boolean networks that are based on a new semantics used in answer set programming (ASP). Our work is based on the enu- meration of all the attractors of asynchronous Boolean networks having interaction graphs which are circuits. We show that the used semantics allows to design a new approach for computing exhaustively both the stable cycles and the stable states of such networks. The enumeration of all the attractors and the distinction between both types of attractors is a significant step to better understand some critical aspects of biology. We applied and evaluated the proposed approach on randomly generated Boolean networks and the obtained results highlight the benefits of this approach, and match with some conjectured results in biology.

Cracking the Egg: Virtual Embryogenesis of Real Robots

2014 ◽  
Vol 20 (3) ◽  
pp. 361-383 ◽  
Author(s):  
Sylvain Cussat-Blanc ◽  
Jordan Pollack
Keyword(s):  
Single Cell ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Process ◽  
Body Plan ◽  
Living Systems ◽  
New Approach ◽  
Virtual Cells ◽  
Building Process ◽  
Gene Regulatory

All multicellular living beings are created from a single cell. A developmental process, called embryogenesis, takes this first fertilized cell down a complex path of reproduction, migration, and specialization into a complex organism adapted to its environment. In most cases, the first steps of the embryogenesis take place in a protected environment such as in an egg or in utero. Starting from this observation, we propose a new approach to the generation of real robots, strongly inspired by living systems. Our robots are composed of tens of specialized cells, grown from a single cell using a bio-inspired virtual developmental process. Virtual cells, controlled by gene regulatory networks, divide, migrate, and specialize to produce the robot's body plan (morphology), and then the robot is manually built from this plan. Because the robot is as easy to assemble as Lego, the building process could be easily automated.

Induced pluripotent stem cell technology: trends in molecular biology, from genetics to epigenetics

Epigenomics ◽  
2021 ◽  
Author(s):  
Amirhosein Maali ◽  
Faezeh Maroufi ◽  
Farzin Sadeghi ◽  
Amir Atashi ◽  
Reza Kouchaki ◽  
...  
Keyword(s):  
Stem Cell ◽  
Molecular Basis ◽  
Regulatory Networks ◽  
Pluripotent Stem Cell ◽  
Induced Pluripotent Stem Cell ◽  
Basic Research ◽  
Retroviral Vectors ◽  
New Approach ◽  
Reprogramming Factors ◽  
Induced Pluripotent

Induced pluripotent stem cell (iPSC) technology, based on autologous cells’ reprogramming to the embryonic state, is a new approach in regenerative medicine. Current advances in iPSC technology have opened up new avenues for multiple applications, from basic research to clinical therapy. Thus, conducting iPSC trials have attracted increasing attention and requires an extensive understanding of the molecular basis of iPSCs. Since iPSC reprogramming is based on the methods inducing the expression of specific genes involved in pluripotency states, it can be concluded that iPSC reprogramming is strongly influenced by epigenetics. In this study, we reviewed the molecular basis of reprogramming, including the reprogramming factors (OCT4, SOX2, KLF4, c-MYC, NANOG, ESRRB, LIN28 as well as their regulatory networks), applied vectors (retroviral vectors, adenoviral vectors, Sendaiviral vectors, episomal plasmids, piggyBac, simple vectors, etc.) and epigenetic modifications (miRNAs, histones and DNA methylation states) to provide a comprehensive guide for reprogramming studies.

scholarly journals Dynamical Modularity of the Genotype-Phenotype Map

2021 ◽  
Author(s):  
Johannes Jaeger ◽  
Nick Monk
Keyword(s):  
Gene Regulatory Networks ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Dynamic Behaviour ◽  
New Approach ◽  
Regulatory Systems ◽  
Alternative Approach ◽  
Gene Regulatory ◽  
And Function ◽  
Discrete Traits

An organism’s phenotype can be thought of as consisting of a set of discrete traits, able to evolve relatively independently of each other. This implies that the developmental processes generating these traits—the underlying genotype-phenotype map—must also be functionally organised in a modular manner. The genotype-phenotype map lies at the heart of evolutionary systems biology. Recently, it has become popular to define developmental modules in terms of the structure of gene regulatory networks. This approach is inherently limited: gene networks often do not have structural modularity. More generally, the connection between structure and function is quite loose. In this chapter, we discuss an alternative approach based on the concept of dynamical modularity, which overcomes many of the limitations of structural modules. A dynamical module consists of the activities of a set of genes and their interactions that generate a specific dynamic behaviour. These modules can be identified and characterised by phase-space analysis of data-driven models. We showcase the power and the promise of this new approach using several case studies. Dynamical modularity forms an important component of a general theory of the evolution of regulatory systems and the genotype-phenotype map they define.

scholarly journals The TF-miRNA Coregulation Network in Oral Lichen Planus

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Yu-Ling Zuo ◽  
Di-Ping Gong ◽  
Bi-Ze Li ◽  
Juan Zhao ◽  
Ling-Yue Zhou ◽  
...  
Keyword(s):  
Lichen Planus ◽  
Regulatory Networks ◽  
Oral Lichen Planus ◽  
Molecular Mechanisms ◽  
Chronic Inflammatory Disease ◽  
New Approach ◽  
Functional Relationships ◽  
Gene Modules ◽  
Gene Regulatory ◽  
Oral Lichen

Oral lichen planus (OLP) is a chronic inflammatory disease that affects oral mucosa, some of which may finally develop into oral squamous cell carcinoma. Therefore, pinpointing the molecular mechanisms underlying the pathogenesis of OLP is important to develop efficient treatments for OLP. Recently, the accumulation of the large amount of omics data, especially transcriptome data, provides opportunities to investigate OLPs from a systematic perspective. In this paper, assuming that the OLP associated genes have functional relationships, we present a new approach to identify OLP related gene modules from gene regulatory networks. In particular, we find that the gene modules regulated by both transcription factors (TFs) and microRNAs (miRNAs) play important roles in the pathogenesis of OLP and many genes in the modules have been reported to be related to OLP in the literature.

The O–C diagrams of minor planets − a new approach to modelling the rotation

1999 ◽  
Vol 173 ◽  
pp. 185-188
Author(s):  
Gy. Szabó ◽  
K. Sárneczky ◽  
L.L. Kiss
Keyword(s):  
Error Analysis ◽  
Time Dependence ◽  
Theoretical Work ◽  
Minor Planet ◽  
Minor Planets ◽  
New Approach ◽  
Preliminary Results ◽  
Ccd Observations

AbstractA widely used tool in studying quasi-monoperiodic processes is the O–C diagram. This paper deals with the application of this diagram in minor planet studies. The main difference between our approach and the classical O–C diagram is that we transform the epoch (=time) dependence into the geocentric longitude domain. We outline a rotation modelling using this modified O–C and illustrate the abilities with detailed error analysis. The primary assumption, that the monotonity and the shape of this diagram is (almost) independent of the geometry of the asteroids is discussed and tested. The monotonity enables an unambiguous distinction between the prograde and retrograde rotation, thus the four-fold (or in some cases the two-fold) ambiguities can be avoided. This turned out to be the main advantage of the O–C examination. As an extension to the theoretical work, we present some preliminary results on 1727 Mette based on new CCD observations.

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