Discovering local patterns of co - evolution: computational aspects and biological examples

Background

Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local.

Results

In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution, signaling pathways that are related to neurotransmission exhibit a relatively higher level of co-evolution along the primate subtree.

Conclusions

We show that finding local patterns of co-evolution is a computationally challenging task and we offer novel algorithms that allow us to solve this problem, thus opening a new approach for analyzing the evolution of biological systems.     

A synergetic model for the verbal transformation effect

We describe a nonlinear dynamical model based on synergetics for the auditory perceptual illusion known as the verbal transformation effect. The model is an extension of a synergetic model of perceptual oscillations of visual ambiguous figures. The main extension is connected to the number of reported alternative phonemic structures, which is typically much greater than the two or three alternatives usually reported in experiments with visual ambiguous figures. The properties of the model, which are derived using basic psychophysical principles, are presented and evaluated on the basis of the fit to earlier empirical work. It will be shown that there is very good agreement between the empirically observed properties of the verbal transformation effect and the properties detected by the model. Received: 19 February 1997 / Accepted in revised form: 27 May 1997     

Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis

Background  

Giardia intestinalis is a parasitic protozoan and major cause of diarrhoeal disease. Disease transmission is dependent on the ability of the parasite to differentiate back and forth between an intestine-colonising trophozoite and an environmentally-resistant infective cyst. Our current understanding of the intracellular signalling mechanisms that regulate parasite replication and differentiation is limited, yet such information could suggest new methods of disease control. Phosphoinositide-3 kinase (PI3K) signalling pathways have a central involvement in many vital eukaryotic processes, such as regulation of cell growth, intracellular membrane trafficking and cell motility. Here we present evidence for the existence of functional PI3K intracellular signalling pathways in G. intestinalis.     

Maternal prenatal depressive symptoms predict infant NR3C1 1F and BDNF IV DNA methylation

Prenatal maternal psychological distress increases risk for adverse infant outcomes. However, the biological mechanisms underlying this association remain unclear. Prenatal stress can impact fetal epigenetic regulation that could underlie changes in infant stress responses. It has been suggested that maternal glucocorticoids may mediate this epigenetic effect. We examined this hypothesis by determining the impact of maternal cortisol and depressive symptoms during pregnancy on infant NR3C1 and BDNF DNA methylation. Fifty-seven pregnant women were recruited during the second or third trimester. Participants self-reported depressive symptoms and salivary cortisol samples were collected diurnally and in response to a stressor. Buccal swabs for DNA extraction and DNA methylation analysis were collected from each infant at 2 months of age, and mothers were assessed for postnatal depressive symptoms. Prenatal depressive symptoms significantly predicted increased NR3C1 1F DNA methylation in male infants (β = 2.147, P = 0.044). Prenatal depressive symptoms also significantly predicted decreased BDNF IV DNA methylation in both male and female infants (β = −3.244, P = 0.013). No measure of maternal cortisol during pregnancy predicted infant NR3C1 1F or BDNF promoter IV DNA methylation. Our findings highlight the susceptibility of males to changes in NR3C1 DNA methylation and present novel evidence for altered BDNF IV DNA methylation in response to maternal depression during pregnancy. The lack of association between maternal cortisol and infant DNA methylation suggests that effects of maternal depression may not be mediated directly by glucocorticoids. Future studies should consider other potential mediating mechanisms in the link between maternal mood and infant outcomes.     

A New Model Describing Solid Oxide Fuel Cell Cathode Kinetics: Model Thin Film SrTi1‐xFexO3‐δ Mixed Conducting Oxides–a Case Study

Identifying the important factors governing the oxygen reduction kinetics at solid oxide fuel cell cathodes is critical for enhanced performance, particularly at reduced temperatures. In this work, a model mixed conducting perovskite materials system, SrTi_1–xFe_xO_3–δ, is selected, offering the ability to systematically control both the levels of ionic and electronic conductivity as well as the energy band structure. This, in combination with considerably simplified electrode geometry, serves to demonstrate that the rate of oxygen exchange at the surface of SrTi_1–xFe_xO_3–δ is only weakly correlated with either high electronic or ionic conductivity, in apparent contradiction with common expectations. Based on the correlation found between the position of the Fermi energy relative to the conduction band edge and the activation energy exhibited by the exchange rate constant, it is possible to confirm experimentally, for the first time, the key role that the minority electronic species play in determining the overall reaction kinetics. These observations lead to a new conceptual model describing cathode kinetics and provide guidelines for identifying cathodes with improved performance.     

Multiple roles of the coding sequence 5′ end in gene expression regulation

The codon composition of the coding sequence''s (ORF) 5′ end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation. However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging. Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.     

Inhibiteurs non acides et dormance embryonnaire chez Taxus baccata

Non-acidic inhibitors and embryo dormancy in Taxus baccata L. Embryo dormancy of Taxus baccata is eliminated when the embryos are continuously kept in sterile nutritive liquid medium. After 3 weeks of culture, an important non-acidic inhibitory complex can be extracted from this liquid medium. At least three substances are involved: two pigments and a compound with some properties that suggest xanthoxin. These substances are neither found in embryos taken directly from the seeds, nor in liquid medium after 8 days of culture, which is the time necessary and sufficient to allow germination after transfer on agar medium. Such behaviour is quite different from that of ABA previously studied and indicates that these non-acidic inhibitors appear late during the culture and are not directly involved in embryo dormancy.