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.

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

Developing roles for Hox proteins in hindbrain gene regulatory networks

2018 ◽  
Vol 62 (11-12) ◽  
pp. 767-774 ◽  
Author(s):  
Priyanjali Ghosh ◽  
Charles G. Sagerström
Keyword(s):  
Functional Analysis ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Transcriptional Regulators ◽  
Hox Proteins ◽  
Recent Advances ◽  
Specific Focus ◽  
Gene Regulatory

Hox proteins have long been known to function as transcriptional regulators during development of the vertebrate hindbrain. In particular, these factors are thought to play key roles in assigning distinct fates to the rhombomere segments arising in the embryonic hindbrain. However, it remains uncertain exactly how the Hox proteins fit into the regulatory networks controlling hindbrain formation. For instance, it is unclear if Hox proteins fulfill similar roles in different rhombomeres and if they are absolutely required for all aspects of each rhombomere fate. Recent advances in the discovery, characterization and functional analysis of hindbrain gene regulatory networks is now allowing us to revisit these types of questions. In this review we focus on recent data on the formation of caudal rhombomeres in vertebrates, with a specific focus on zebrafish, to derive an up-to-date view of the role for Hox proteins in the regulation of hindbrain development.

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.

Dynamic Links and Evolutionary History in Simulated Gene Regulatory Networks

2010 ◽  
pp. 498-522
Author(s):  
T. Steiner ◽  
Y. Jin ◽  
L. Schramm ◽  
B. Sendhoff
Keyword(s):  
Gene Regulatory Networks ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Evolutionary Process ◽  
Computational Method ◽  
Cellular Growth ◽  
Small Scale ◽  
Mutational Robustness ◽  
Gene Regulatory ◽  
Artificial Gene

In this chapter, we describe the use of evolutionary methods for the in silico generation of artificial gene regulatory networks (GRNs). These usually serve as models for biological networks and can be used for enhancing analysis methods in biology. We clarify our motivation in adopting this strategy by showing the importance of detailed knowledge of all processes, especially the regulatory dynamics of interactions undertaken during gene expression. To illustrate how such a methodology works, two different approaches to the evolution of small-scale GRNs with specified functions, are briefly reviewed and discussed. Thereafter, we present an approach to evolve medium sized GRNs with the ability to produce stable multi-cellular growth. The computational method employed allows for a detailed analysis of the dynamics of the GRNs as well as their evolution. We have observed the emergence of negative feedback during the evolutionary process, and we suggest its implication to the mutational robustness of the regulatory network which is further supported by evidence observed in additional experiments.

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