Molecular Biology and Functional Genomics for Identification of Regulatory Networks of Plant Sulfate Uptake and Assimilatory Metabolism

2008 ◽  
pp. 149-159 ◽  
Author(s):  
Hideki Takahashi ◽  
Kazuki Saito
Keyword(s):  
Molecular Biology ◽  
Functional Genomics ◽  
Regulatory Networks ◽  
Sulfate Uptake

Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics

2021 ◽  
Vol 22 ◽  
Author(s):  
Soma Ghosh ◽  
Malathi Bheri ◽  
Girdhar K. Pandey
Keyword(s):  
Functional Genomics ◽  
Protein Kinases ◽  
Regulatory Networks ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Major Elements ◽  
Model Systems ◽  
Plant Responses ◽  
Dependent Protein

: Plant systems have developed calcium (Ca2+) signaling as an important mechanism of regulation of stress perception, developmental cues, and responsive gene expression. The post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery involve Ca2+ sensors and responders such as Calmodulin (CaM), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMK), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be the stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

Computational studies of gene regulatory networks: in numero molecular biology

2001 ◽  
Vol 2 (4) ◽  
pp. 268-279 ◽  
Author(s):  
Jeff Hasty ◽  
David McMillen ◽  
Farren Isaacs ◽  
James J. Collins
Keyword(s):  
Molecular Biology ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Computational Studies ◽  
Gene Regulatory

Systems Biology and Infectious Diseases

2009 ◽  
pp. 377-402 ◽  
Author(s):  
Alia Benkahla ◽  
Lamia Guizani-Tabbane ◽  
Ines Abdeljaoued-Tej ◽  
Slimane Ben Miled ◽  
Koussay Dellagi
Keyword(s):  
Immune Response ◽  
Systems Biology ◽  
Molecular Biology ◽  
Infected Cell ◽  
Regulatory Networks ◽  
Interdisciplinary Approach ◽  
Biochemical Networks ◽  
Mathematical Methods ◽  
Meaningful Information ◽  
Models And Modelling

This chapter reports a variety of molecular biology informatics and mathematical methods that model the cell response to pathogens. The authors first outline the main steps of the immune response, then list the high throughput biotechnologies, generating a wealth of information on the infected cell and some of the immune-related databases; and finally explain how to extract meaningful information from these sources. The modelling aspect is divided into modelling molecular interaction and regulatory networks, through dynamic Boolean and Bayesian models, and modelling biochemical networks and regulatory networks, through Differential/Difference Equations. The interdisciplinary approach explains how to construct a model that mimics the cell’s dynamics and can predict the evolution and the outcome of infection.

scholarly journals Computational Methodologies for Analyzing, Modeling and Controlling Gene Regulatory Networks

2010 ◽  
Vol 2 ◽  
pp. BECB.S5594 ◽  
Author(s):  
Zahra Zamani ◽  
Amirhossein Hajihosseini ◽  
Ali Masoudi-Nejad
Keyword(s):  
Molecular Biology ◽  
Computational Methods ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
The Other ◽  
Therapeutic Interventions ◽  
Control Network ◽  
Deep Insight ◽  
Paper Briefly ◽  
Gene Regulatory

Molecular biology focuses on genes and their interactions at the transcription, regulation and protein level. Finding genes that cause certain behaviors can make therapeutic interventions more effective. Although biological tools can extract the genes and perform some analyses, without the help of computational methods, deep insight of the genetic function and its effects will not occur. On the other hand, complex systems can be modeled by networks, introducing the main data as nodes and the links in-between as the transactions occurring within the network. Gene regulatory networks are examples that are modeled and analyzed in order to gain insight of their exact functions. Since a cell's specific functionality is greatly determined by the genes it expresses, translation or the act of converting mRNA to proteins is highly regulated by the control network that directs cellular activities. This paper briefly reviews the most important computational methods for analyzing, modeling and controlling the gene regulatory networks.

Molecular biology and functional genomics of liver X receptors (LXR) in relationship to metabolic diseases

2010 ◽  
Vol 10 (6) ◽  
pp. 692-697 ◽  
Author(s):  
Malin Hedengran Faulds ◽  
Chunyan Zhao ◽  
Karin Dahlman-Wright
Keyword(s):  
Molecular Biology ◽  
Functional Genomics ◽  
Metabolic Diseases ◽  
Liver X Receptors ◽  
X Receptors

scholarly journals Molecular Paleobiology of the Echinoderm Skeleton

2022 ◽  
Author(s):  
Jeffrey Thompson
Keyword(s):  
Molecular Biology ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Evolutionary Process ◽  
Functional Genomic ◽  
Deep Time ◽  
Recent Advances ◽  
Gene Regulatory ◽  
Multiple Levels ◽  
Promising Avenue

Molecular paleobiology provides a promising avenue to merge data from deep time, molecular biology and genomics, gaining insights into the evolutionary process at multiple levels. The echinoderm skeleton is a model for molecular paleobioloogical studies. I begin with an overview of the skeletogenic process in echinoderms, as well as a discussion of what gene regulatory networks are, and why they are of interest to paleobiologists. I then highlight recent advances in the evolution of the echinoderm skeleton from both paleobiological and molecular/functional genomic perspectives, highlighting examples where diverse approaches provide complementary insight and discussing potential of this field of research.

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