scholarly journals The Protein-Protein Interaction Networks of Dendritic Spines in the Early Phase of Long-Term Potentiation

2014 ◽  
Vol 7 (1) ◽  
Author(s):  
Anna L Proskura
Keyword(s):  
Protein Interaction ◽  
Dendritic Spines ◽  
Early Phase ◽  
Long Term Potentiation ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Term Potentiation ◽  
Protein Protein Interaction Networks

scholarly journals Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Sandip Chakraborty ◽  
David Alvarez-Ponce
Keyword(s):  
Positive Selection ◽  
Protein Interaction ◽  
Interaction Network ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks ◽  
Interspecific Comparisons ◽  
High Degree

Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins) are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons) tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

scholarly journals Prenatal testosterone triggers long-term behavioral changes in male zebra finches: unravelling the neurogenomic mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexandra B. Bentz ◽  
Chad E. Niederhuth ◽  
Laura L. Carruth ◽  
Kristen J. Navara
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Zebra Finches ◽  
Hub Genes ◽  
Prenatal Testosterone ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

Abstract Background Maternal hormones, like testosterone, can strongly influence developing offspring, even generating long-term organizational effects on adult behavior; yet, the mechanisms facilitating these effects are still unclear. Here, we experimentally elevated prenatal testosterone in the eggs of zebra finches (Taeniopygia guttata) and measured male aggression in adulthood along with patterns of neural gene expression (RNA-seq) and DNA methylation (MethylC-Seq) in two socially relevant brain regions (hypothalamus and nucleus taenia of the amygdala). We used enrichment analyses and protein-protein interaction networks to find candidate processes and hub genes potentially affected by the treatment. We additionally identified differentially expressed genes that contained differentially methylated regions. Results We found that males from testosterone-injected eggs displayed more aggressive behaviors compared to males from control eggs. Hundreds of genes were differentially expressed, particularly in the hypothalamus, including potential aggression-related hub genes (e.g., brain derived neurotrophic factor). There were also enriched processes with well-established links to aggressive phenotypes (e.g., somatostatin and glutamate signaling). Furthermore, several highly connected genes identified in protein-protein interaction networks also showed differential methylation, including adenylate cyclase 2 and proprotein convertase 2. Conclusions These results highlight genes and processes that may play an important role in mediating the effects of prenatal testosterone on long-term phenotypic outcomes, thereby providing insights into the molecular mechanisms that facilitate hormone-mediated maternal effects.

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