Biological networks, such as gene regulatory networks, possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated into biological networks. A recent meta-analysis of published, expert-curated Boolean biological network models has revealed several such features, often referred to as design principles. Among others, the biological networks are enriched for certain recurring network motifs, the dynamic update rules are more redundant, more biased, and more canalizing than expected, and the dynamics of biological networks are better approximable by linear and lower-order approximations than those of comparable random networks. Since most of these features are interrelated, it is paramount to disentangle cause and effect, that is, to understand which features evolution actively selects for, and thus truly constitute evolutionary design principles. Here, we compare published Boolean biological network models with different ensembles of null models and show that the abundance of canalization in biological networks can almost completely explain their recently postulated high approximability. Moreover, an analysis of random N-K Kauffman models reveals a strong dependence of approximability on the dynamical robustness of a network.
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http://dx.doi.org/10.1038/s41540-024-00392-y | DOI Listing |
Inflamm Res
January 2025
Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil.
Introduction: The present study aimed at evaluating the systemic profile and network connectivity of immune mediators during acute chikungunya fever (CHIKF) according to days of symptoms onset and ageing.
Methods: A total of 161 volunteers (76 CHIKF patients and 85 non-infected healthy controls) were enrolled.
Results And Discussion: Data demonstrated that a massive and polyfunctional storm of serum immune mediators was observed in CHIKF.
Theor Appl Genet
January 2025
Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.
Phenomic selection based on parental spectra can be used to predict GCA and SCA in a sparse factorial design. Prediction approaches such as genomic selection can be game changers in hybrid breeding. They allow predicting the genetic values of hybrids without the need for their physical production.
View Article and Find Full Text PDFPlant Physiol
January 2025
Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, College of Horticulture, Hunan Agricultural University, Changsha 410125, China.
Carotenoids play indispensable roles in the ripening process of fleshy fruits. Capsanthin is a widely distributed and utilized natural red carotenoid. However, the regulatory genes involved in capsanthin biosynthesis remain insufficient.
View Article and Find Full Text PDFGenes Dev
December 2024
Institute for Diabetes, Obesity, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19146, USA;
The Cullin-3 E3 ligase adaptor protein SPOP targets proteins for ubiquitination and proteasomal degradation. We previously established the β-cell transcription factor (TF) and human diabetes gene PDX1 as an SPOP substrate, suggesting a functional role for SPOP in the β cell. Here, we generated a β-cell-specific deletion mouse strain ( ) and found that is necessary to prevent aberrant basal insulin secretion and for maintaining glucose-stimulated insulin secretion through impacts on glycolysis and glucose-stimulated calcium flux.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, NO.1800, Lihu avenue, Wuxi 214122, China.
Inducible systems are crucial to metabolic engineering and synthetic biology, enabling organisms that function as biosensors and produce valuable compounds. However, almost all inducible systems are strain-specific, limiting comparative analyses and applications across strains rapidly. This study designed and presented a robust workflow for developing the cross-species inducible system.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!