Hierarchy and Feedback in the Evolution of the E. coli Transcription Network

The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of gene duplication based on protein domain architecture shows that (i) transcriptional autoregulators have mostly arisen through duplication, while (ii) the expected feedback loops stemming from their initial cross-regulation are strongly selected against. This requires a divergent coevolution of the transcription factor DNA-binding sites and their respective DNA cis-regulatory regions. Moreover, we find that the network tends to grow by expansion of the existing hierarchical layers of computation, rather than by addition of new layers. We also argue that rewiring of regulatory links due to mutation/selection of novel transcription factor/DNA binding interactions appears not to significantly affect the network global hierarchy, and that horizontally transferred genes are mainly added at the bottom, as new target nodes. These findings highlight the important evolutionary roles of both duplication and selective deletion of crosstalks between autoregulators in the emergence of the hierarchical transcription network of E.coli.Comment: to appear in PNA

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology

Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive evolutionary forces. Teasing apart these forces is an important step toward functional analyses of the different components of CRNs, designing regulatory perturbation experiments, and constructing synthetic networks. Although tests of neutrality and selection based on molecular sequence data exist, no such tests are currently available based on CRNs. In this work, we present a unique genotype model of CRNs that is grounded in a genomic context and demonstrate its use in identifying portions of the CRN with properties explainable by neutral evolutionary forces at the system, subsystem, and operon levels.We leverage our model against experimentally derived data from Escherichia coli. The results of this analysis show statistically significant and substantial neutral trends in properties previously identified as adaptive in originﾗdegree distribution, clustering coefficient, and motifsﾗ within the E. coli CRN. Our model captures the tightly coupled genomeﾖ interactome of an organism and enables analyses of how evolutionary events acting at the genome level, such as mutation, and at the population level, such as genetic drift, give rise to neutral patterns that we can quantify in CRNs

Degeneracy: a link between evolvability, robustness and complexity in biological systems

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability

Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems

A generic mechanism - networked buffering - is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems. \ud \u

Three-dimensional simulations of inorganic aerosol distributions in east Asia during spring 2001

In this paper, aerosol composition and size distributions in east Asia are simulated using a comprehensive chemical transport model. Three-dimensional aerosol simulations for the TRACE-P and ACE-Asia periods are performed and used to help interpret actual observations. The regional chemical transport model, STEM-2K3, which includes the on-line gas-aerosol thermodynamic module SCAPE II, and explicitly considers chemical aging of dust, is used in the analysis. The model is found to represent many of the important observed features. The Asian outflow during March and April of 2001 is heavily polluted with high aerosol loadings. Under conditions of low dust loading, SO_2 condensation and gas phase ammonia distribution determine the nitrate size and gas-aerosol distributions along air mass trajectories, a situation that is analyzed in detail for two TRACE-P flights. Dust is predicted to alter the partitioning of the semivolatile components between the gas and aerosol phases as well as the size distributions of the secondary aerosol constituents. Calcium in the dust affects the gas-aerosol equilibrium by shifting the equilibrium balance to an anion-limited status, which benefits the uptake of sulfate and nitrate, but reduces the amount of aerosol ammonium. Surface reactions on dust provide an additional mechanism to produce aerosol nitrate and sulfate. The size distribution of dust is shown to be a critical factor in determining the size distribution of secondary aerosols. As much of the dust mass is found in the supermicron mode (70–90%), appreciable amounts of sulfate and nitrate are found in the supermicron particles. For sulfate the observations and the analysis indicate that 10–30% of sulfate is in the supermicron fraction during dust events; in the case of nitrate, more than 80% is found in the supermicron fraction

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table 9 published in 10.1371/journal.pone.0017244. Supporting information is attached at the end of the article, and a computer-readable dataset of the ML estimates of selective constraints is available from 10.1371/journal.pone.001724

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Effect of human immunodeficiency virus on blood-brain barrier integrity and function: an update

The blood-brain barrier (BBB) is a diffusion barrier that has an important role in maintaining a precisely regulated microenvironment protecting the neural tissue from infectious agents and toxins in the circulating system. Compromised BBB integrity plays a major role in the pathogenesis of retroviral associated neurological diseases. Human Immunodeficiency Virus (HIV) infection in the Central Nervous System (CNS) is an early event even before the serodiagnosis for HIV positivity or the initiation of antiretroviral therapy (ART), resulting in neurological complications in many of the infected patients. Macrophages, microglia and astrocytes (in low levels) are the most productively/latently infected cell types within the CNS. In this brief review, we have discussed about the effect of HIV infection and viral proteins on the integrity and function of BBB, which may contribute to the progression of HIV associated neurocognitive disorders

Pesan Moral Islami Dalam Film Le Grand Voyage Karya Ismael Ferroukhi: Sebuah Tinjauan Struktural

Kata kunci : Film, sastra, struktural, pesan moral, Islam.Film merupakan produk budaya yang tidak hanya menjadi hiburan di masyarakat, tetapi juga sebagai sarana penyampaian pesan moral yang mengarifkan. Salah satufilm Perancis yang dianggap menginspirasi adalah film berjudul Le grand voyageyang ditulis dan disutradarai oleh Ismaël Ferroukhi. Film ini bercerita tentang perjalanan seorang muslim keturunan Maroko dan anaknya yang bernama Reda.Mereka menempuh jarak ribuan mil dari Perancis menuju ke kota Makah untukmelaksanakan haji hanya dengan mengendarai sebuah mobil tua. Penelitian inibertujuan untuk mengetahui pesan moral islami apa saja yang terkandung dalamfilm Le grand voyage dan bagaimana pesan tersebut dimunculkan dalam film.Penelitian ini menggunakan teori Struktural untuk menjawab rumusan masalah.Penelitian ini merupakan penelitian kualitatif dengan menggunakan teknik studipustaka serta dokumentasi sebagai metode pengumpulan data, dan teknikdeskriptif dalam proses analisis data.Berdasarkan hasil penelitian ini, terdapat 13 pesan moral islami yang terkandungdalam film Le grand voyage. Semua pesan moral tersebut mengacu pada sebuahproses perbaikan moral dan spiritual antara manusia dengan manusia dan alam,serta antara manusia dengan TuhanPenulis menyarankan pada penelitian selanjutnya untuk meneliti film Le grandvoyage menggunakan pendekatan sosiologi sastra yang nantinya dapat mengupashal apa saja yang melatarbelakangi pembuatan film ini dan tujuan sebenarnyayang ingin dicapai oleh pembuat film Le grand voyage

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life