Reaction Network Models as a Tool to Study Gene Regulation and Cell Signaling in Development and Diseases

2020 ◽  
pp. 119-159
Author(s):  
Francisco José Pereira Lopes ◽  
Claudio Daniel Tenório de Barros ◽  
Josué Xavier de Carvalho ◽  
Fernando de Magalhães Coutinho Vieira ◽  
Cristiano N. Costa
Keyword(s):  
Gene Regulation ◽  
Cell Signaling ◽  
Reaction Network ◽  
Network Models ◽  
Study Gene Regulation

scholarly journals Chemical Reporters and Their Bioorthogonal Reactions for Labeling Protein O-GlcNAcylation

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2411
Author(s):  
Eun Kim
Keyword(s):  
Gene Regulation ◽  
Molecular Biology ◽  
Cell Signaling ◽  
Molecular Tools ◽  
Bioorthogonal Reactions ◽  
Cytoplasmic Proteins ◽  
Mechanistic View ◽  
New Strategies

Protein O-GlcNAcylation is a non-canonical glycosylation of nuclear, mitochondrial, and cytoplasmic proteins with the attachment of a single O-linked β-N-acetyl-glucosamine (O-GlcNAc) moiety. Advances in labeling and identifying O-GlcNAcylated proteins have helped improve the understanding of O-GlcNAcylation at levels that range from basic molecular biology to cell signaling and gene regulation to physiology and disease. This review describes these advances in chemistry involving chemical reporters and their bioorthogonal reactions utilized for detection and construction of O-GlcNAc proteomes in a molecular mechanistic view. This detailed view will help better understand the principles of the chemistries utilized for biology discovery and promote continued efforts in developing new molecular tools and new strategies to further explore protein O-GlcNAcylation.

scholarly journals Building reaction kinetic models for amiloid fibril growth

BIOMATH ◽  
2016 ◽  
Vol 5 (1) ◽  
pp. 1607311 ◽  
Author(s):  
Svetoslav Marinov Markov
Keyword(s):  
Computer Algebra ◽  
Computer Algebra System ◽  
Reaction Kinetic ◽  
Growth Models ◽  
Reaction Network ◽  
Network Models ◽  
Point Of View ◽  
Logistic Growth ◽  
Sigmoidal Functions ◽  
Methodological Aspects

In this work we  discuss some methodological aspects of the creation and formulation of mathematical  models describing the growth of species from the point of view of reaction kinetics. Our discussion is based on familiar examples of growth models such as logistic growth and enzyme kinetics. We   propose several reaction network  models  for  the amiloid fibrillation processes in the citoplasm. The solutions of the models are sigmoidal functions graphically visualized using  the computer algebra system   Mathematica.

IDENTIFYING CHEMICAL REACTION NETWORK MODELS

2007 ◽  
Vol 40 (5) ◽  
pp. 225-230 ◽  
Author(s):  
S.C. Burnham ◽  
M.J. Willis ◽  
A.R Wright
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Network Models ◽  
Chemical Reaction Network

scholarly journals Hematopoietic Differentiation of Embryonic Stem Cells: An In Vitro Model to Study Gene Regulation during Megakaryocytopoiesis

Stem Cells ◽  
1996 ◽  
Vol 14 (S1) ◽  
pp. 194-199 ◽  
Author(s):  
Georges Uzan ◽  
Marie‐Hélène Prandini ◽  
Jean‐Philippe Rosa ◽  
Rolande Berthier
Keyword(s):  
Stem Cells ◽  
Gene Regulation ◽  
Embryonic Stem Cells ◽  
In Vitro Model ◽  
Embryonic Stem ◽  
Hematopoietic Differentiation ◽  
Vitro Model ◽  
Study Gene Regulation

A two-stage inference algorithm for gene regulation network models

2016 ◽  
Vol 9 (1/2) ◽  
pp. 6
Author(s):  
Alexandru Mizeranschi ◽  
Huiru Zheng ◽  
Paul Thompson ◽  
Werner Dubitzky
Keyword(s):  
Gene Regulation ◽  
Network Models ◽  
Inference Algorithm ◽  
Two Stage ◽  
Gene Regulation Network ◽  
Regulation Network

Cell signaling and gene regulation

2012 ◽  
Vol 15 (5) ◽  
pp. 493-495
Author(s):  
Jerzy Paszkowski ◽  
Robert A Martienssen
Keyword(s):  
Gene Regulation ◽  
Cell Signaling
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