How do regulatory networks evolve and expand throughout evolution?

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Regions of multistationarity in cascades of Goldbeter–Koshland loops

Journal of Mathematical Biology - We consider cascades of enzymatic Goldbeter–Koshland loops (Goldbeter and Koshland in Proc Natl Acad Sci 78(11):6840–6844, 1981) with any number n of...     

Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies

Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary computational circuits has been cause for debate. As the question is difficult to resolve with currently available biological data, we approach the issue using networks that abstractly model natural genetic regulatory networks (GRNs) which are evolved to show dynamical behaviors. Specifically one group of networks was evolved to be capable of exhibiting two different behaviors ("differentiation") in contrast to a group with a single target behavior. In both groups we find motif distribution differences within the groups to be larger than differences between them, indicating that evolutionary niches (target functions) do not necessarily mold network structure uniquely. These results show that variability operators can have a stronger influence on network topologies than selection pressures, especially when many topologies can create similar dynamics. Moreover, analysis of motif functional relevance by lesioning did not suggest that motifs were of greater importance to the functioning of the network than arbitrary subgraph patterns. Only when drastically restricting network size, so that one motif corresponds to a whole functionally evolved network, was preference for particular connection patterns found. This suggests that in non-restricted, bigger networks, entanglement with the rest of the network hinders topological subgraph analysis.     

How robust are switches in intracellular signaling cascades?

Since all-or-none decisions of the cell are controlled by extracellular signals, cells have biochemical switches within their intracellular signaling networks. Central elements of these switches are multisite phosphorylation, enzymic saturation, and amplification by cascades. Moreover, positive feedback can contribute to switch-like behavior termed also ultrasensitivity. Here we analyse the robustness of these mechanisms exemplified by models of the three-molecule MAPK-cascade and the single-molecule Goldbeter-Koshland switch. We show that the ultrasensitivity in the MAPK-cascades is more robust against changes of the kinetic parameters than the Goldbeter-Koshland switch. If multiple parameters are changed randomly, the effects of parameter changes can compensate each other in the cascade leading to a remarkable robustness of the switch-like behavior. The different degrees of robustness can be traced back to the different mechanisms of generating ultrasensitivity. While in the Goldbeter-Koshland switch the saturation of the enzymes are crucial, in the MAPK-cascade the adjustment of working ranges determines the ultrasensitivity. Our results indicate that amplification of ultrasensitivity in cascades and multisite phosphorylation might be a design principle to achieve robust switches.     

The evolution of endothermy in terrestrial vertebrates: Who? When? Why?

Avian and mammalian endothermy results from elevated rates of resting, or routine, metabolism and enables these animals to maintain high and stable body temperatures in the face of variable ambient temperatures. Endothermy is also associated with enhanced stamina and elevated capacity for aerobic metabolism during periods of prolonged activity. These attributes of birds and mammals have greatly contributed to their widespread distribution and ecological success. Unfortunately, since few anatomical/physiological attributes linked to endothermy are preserved in fossils, the origin of endothermy among the ancestors of mammals and birds has long remained obscure. Two recent approaches provide new insight into the metabolic physiology of extinct forms. One addresses chronic (resting) metabolic rates and emphasizes the presence of nasal respiratory turbinates in virtually all extant endotherms. These structures are associated with recovery of respiratory heat and moisture in animals with high resting metabolic rates. The fossil record of nonmammalian synapsids suggests that at least two Late Permian lineages possessed incipient respiratory turbinates. In contrast, these structures appear to have been absent in dinosaurs and nonornithurine birds. Instead, nasal morphology suggests that in the avian lineage, respiratory turbinates first appeared in Cretaceous ornithurines. The other approach addresses the capacity for maximal aerobic activity and examines lung structure and ventilatory mechanisms. There is no positive evidence to support the reconstruction of a derived, avian-like parabronchial lung/air sac system in dinosaurs or nonornithurine birds. Dinosaur lungs were likely heterogenous, multicameral septate lungs with conventional, tidal ventilation, although evidence from some theropods suggests that at least this group may have had a hepatic piston mechanism of supplementary lung ventilation. This suggests that dinosaurs and nonornithurine birds generally lacked the capacity for high, avian-like levels of sustained activity, although the aerobic capacity of theropods may have exceeded that of extant ectotherms. The avian parabronchial lung/air sac system appears to be an attribute limited to ornithurine birds.     

Parasitic diseases in marine cage culture--an example of experimental evolution of parasites?

Rapid development of fish culture in marine cages has been associated with an emergence of parasitic diseases. There is a general trend to an increase in infections with ectoparasites with direct life cycles and a reduced diversity of parasites in aquaculture. Some mariculture creates conditions that are similar to serial passage experiments, which are used to study adaptation during experimental evolution of pathogens. In particular, increased density of fish, repeated introduction of naive hosts, homogenous host populations, fast growth and a potential decrease in genetic diversity are attributes of both aquaculture and serial passage experiments. Some free-living organisms, for example Neoparamoeba spp. and Uronema spp. parasitise fish in culture, but have not been reported from wild populations. Farming fish in marine cages can increase the risk of outbreaks of parasitic diseases, including those caused by opportunistic parasites. However, aquaculture has the potential to control parasitic diseases through selective breeding, vaccination and general fish health management.     

Human evolution: a legacy of cannibalism in our genes?

A new study of genetic variation in the human prion protein gene suggests that balancing selection has operated on an amino acid sequence polymorphism in the gene during the last five hundred thousand years. Is this a legacy of widespread cannibalism by our ancestors?     

Head shape evolution in Gymnophthalmidae: does habitat use constrain the evolution of cranial design in fossorial lizards?

Habitat usage comprises interactions between ecological parameters and organismal capacities, and the selective pressures that ultimately determine the outcome of such processes in an evolutionary scale may be conflicting when the same morphological structure is recruited for different activities. Here, we investigate the roles of diet and locomotion in the evolution of cranial design in gymnophthalmid lizards and test the hypothesis that microhabitat use drives head shape evolution, particularly in head-first burrowers. Morphological factors were analysed in relation to continuous ecological indexes (prey hardness and substrate compactness) using conventional and phylogenetic approaches. Results suggest that the evolution of head morphology in Gymnophthalmidae was shaped under the influence of microhabitat use rather than diet: burrowers have shorter heads with lower rostral angulation, independently of the prey consumed. Food preferences appear to be relatively conserved throughout the phylogeny of the group, which may have permitted the extensive radiation of gymnophthalmids into fossorial microhabitats.     

T regulatory cells: aid or hindrance in the clearance of disease?

CD4+ CD25+ T regulatory cells (Tregs) are classified as a subset of T cells whose role is the suppression and regulation of immune responses to self and non-self. Since their discovery in the early 1970s, the role of CD4+ CD25+ Tregs in both autoimmune and infectious disease has continued to expand. This review examines the recent advances on the role CD4+ CD25+ Tregs may be playing in various diseases regarding progression or protection. In addition, advances made in the purification and manipulation of CD4+ CD25+ Tregs using new cell markers, techniques and antibodies are discussed. Ultimately, an overall understanding of the exact mechanism which CD4+ CD25+ Tregs implement during disease progression will enhance our ability to manipulate CD4+ CD25+ Tregs in a clinically beneficial manner.     

Are allozymes differing in substrate specificity involved in the evolution of Silene species?

Summary The concerted action of two flavone-skeleton modifying genes, P and Me, and the alleles of three independently segregating loci g, gl and fg involved in flavone-glycosylation lead to the 33 different flavones so far identified in Silene. The alleles of the different loci involved in flavone-glycosylation control enzymes which differ in substrate specificity, a phenomenon not often described in higher organisms. The alleles of the different loci are variously distributed over the different species. The possible evolutionary implications of these distributions are discussed.     

Role of α-fetoprotein in differentiation of regulatory T lymphocytes

The effect of native α-fetoprotein (AFP) on the expression of T-regulatory lymphocyte (Treg) markers by activated CD4⁺ lymphocytes with different proliferative status was studied. α-Fetoprotein did not affect the ratio of proliferating and non-proliferating activated CD4⁺ cells. In the study of Treg differentiation, it was found that AFP at concentrations of 50 and 100 μg/mL significantly inhibited the number of nonproliferating CD4⁺FOXP3⁺ and CD4⁺FOXP3⁺HELIOS⁺ lymphocytes without affecting the expression of Treg markers by proliferating CD4⁺ lymphocytes.     

Are ant supercolonies crucibles of a new major transition in evolution?

The biological hierarchy of genes, cells, organisms and societies is a fundamental reality in the living world. This hierarchy of entities did not arise ex nihilo at the origin of life, but rather has been serially generated by a succession of critical events known as ‘evolutionary transitions in individuality’ (ETIs). Given the sequential nature of ETIs, it is natural to look for candidates to form the next hierarchical tier. We analyse claims that these candidates are found among ‘supercolonies’, ant populations in which discrete nests cooperate as part of a wider collective, in ways redolent of cells in a multicellular organism. Examining earlier empirical work and new data within the recently proposed ‘Darwinian space’ framework, we offer a novel analysis of the evolutionary status of supercolonies and show how certain key conditions might be satisfied in any future process transforming these collaborative networks into true Darwinian individuals.     

From Eden to a hell of uniformity? directed evolution in humans

For the first time during evolution of life on this planet, a species has acquired the ability to direct its own genetic destiny. Following 200,000 years of evolution, modern man now has the technologies not only to eradicate genetic disease but also to prolong life and enhance desired physical and mental traits. These technologies include preimplantation diagnosis, cloning, and gene therapy in the germline on native chromosomes or by adding artificial ones. At first glance, we should all be in favor of eliminating genetic diseases and enhancing genetic traits. Evolutionary considerations, however, uncover hidden dangers and suggest caution against the total embracement of such actions. The first major concern is that the genome will never be a completely reliable crystal ball for predicting human phenotypes. This is especially true for predictions concerning the performance of alleles in future generations whose populations might be subjected to different environmental and social challenges. The second, and perhaps more important, concern is that the end result of germline intervention and genetic enhancement will likely lead to the impoverishment of gene variants in the human population and deprive us of one of our most valued assets for survival in the future, our genetic diversity.