Evolution of cooperation in multichannel games on multiplex networks.

Humans navigate diverse social relationships and concurrently interact across multiple social contexts. An individual's behavior in one context can influence behavior in other contexts. Different payoffs associated with interactions in the different domains have motivated recent studies of the evolution of cooperation through the analysis of multichannel games where each individual is simultaneously engaged in multiple repeated games.

The RNA-DNA world and the emergence of DNA-encoded heritable traits.

The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme.

The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity.

The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes.

Network rewiring promotes cooperation in an aspirational learning model.

We analyze a cooperative decision-making model that is based on individual aspiration levels using the framework of a public goods game in static and dynamic networks. Sensitivity to differences in payoff and dynamic aspiration levels modulates individual satisfaction and affects subsequent behavior. The collective outcome of such strategy changes depends on the efficiency with which aspiration levels are updated.

Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world.

The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands.

How strategy environment and wealth shape altruistic behaviour: cooperation rules affecting wealth distribution in dynamic networks.

Societies rely on individual contributions to sustain public goods that benefit the entire community. Several mechanisms, that specify how individuals change their decisions based on past experiences, have been proposed to explain how altruists are not outcompeted by selfish counterparts. A key aspect of such strategy updates involves a comparison of an individual's latest payoff with that of a random neighbour.

Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth.

The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support.

The evolution of antibiotic production rate in a spatial model of bacterial competition.

We consider competition between antibiotic producing bacteria, non-producers (or cheaters), and sensitive cells in a two-dimensional lattice model. Previous work has shown that these three cell types can survive in spatial models due to the presence of spatial patterns, whereas coexistence is not possible in a well-mixed system. We extend this to consider the evolution of the antibiotic production rate, assuming that the cost of antibiotic production leads to a reduction in growth rate of the producers.

Bribery games on interdependent complex networks.

Bribe demands present a social conflict scenario where decisions have wide-ranging economic and ethical consequences. Nevertheless, such incidents occur daily in many countries across the globe. Harassment bribery constitute a significant sub-set of such bribery incidents where a government official demands a bribe for providing a service to a citizen legally entitled to it.

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi.

Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes.

Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.

Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative genomics studies of riboswitches focusing on their gross distribution across different bacterial taxa have been carried out recently, systematic functional annotation and analysis of lysine riboswitches and the genes they regulate are still lacking.

Bribery games on inter-dependent regular networks.

We examine a scenario of social conflict that is manifest during an interaction between government servants providing a service and citizens who are legally entitled to the service, using evolutionary game-theory in structured populations characterized by an inter-dependent network. Bribe-demands by government servants during such transactions, called harassment bribes, constitute a widespread form of corruption in many countries. We investigate the effect of varying bribe demand made by corrupt officials and the cost of complaining incurred by harassed citizens, on the proliferation of corrupt strategies in the population.

Deciphering a survival strategy during the interspecific competition between MSM-S1 and sp. MSM-M1.

Interspecific competition in bacteria governs colony growth dynamics and pattern formation. Here, we demonstrate an interesting phenomenon of interspecific competition between MSM-S1 and sp MSM-M1, where secretion of an inhibitor by sp is used as a strategy for survival. Although grows faster than sp.

Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code.

The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population.

Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences.

Unlabelled: Riboswitches are non-coding RNA located in the 5' untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity.

An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additional eukaryotic riboswitches since more than 20 riboswitch classes have been found in prokaryotes but only one class has been found in eukaryotes.

Bribe and Punishment: An Evolutionary Game-Theoretic Analysis of Bribery.

Harassment bribes, paid by citizens to corrupt officers for services the former are legally entitled to, constitute one of the most widespread forms of corruption in many countries. Nation states have adopted different policies to address this form of corruption. While some countries make both the bribe giver and the bribe taker equally liable for the crime, others impose a larger penalty on corrupt officers.

Pathways of Genetic Code Evolution in Ancient and Modern Organisms.

There have been two distinct phases of evolution of the genetic code: an ancient phase--prior to the divergence of the three domains of life, during which the standard genetic code was established--and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly from the standard code. Here we discuss the factors that are most important in these two phases, and we argue that these are substantially different. In the modern phase, changes are driven by chance events such as tRNA gene deletions and codon disappearance events.

Two perspectives on the origin of the standard genetic code.

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other.

Revisiting the physico-chemical hypothesis of code origin: an analysis based on code-sequence coevolution in a finite population.

The origin of the genetic code marked a major transition from a plausible RNA world to the world of DNA and proteins and is an important milestone in our understanding of the origin of life. We examine the efficacy of the physico-chemical hypothesis of code origin by carrying out simulations of code-sequence coevolution in finite populations in stages, leading first to the emergence of ten amino acid code(s) and subsequently to 14 amino acid code(s). We explore two different scenarios of primordial code evolution.

Phylogenetic analysis and comparative genomics of purine riboswitch distribution in prokaryotes.

Riboswitches are regulatory RNA that control gene expression by undergoing conformational changes on ligand binding. Using phylogenetic analysis and comparative genomics we have been able to identify the class of genes/operons regulated by the purine riboswitch and obtain a high-resolution map of purine riboswitch distribution across all bacterial groups. In the process, we are able to explain the absence of purine riboswitches upstream to specific genes in certain genomes.

Stuttering Min oscillations within E. coli bacteria: a stochastic polymerization model.

We have developed a 3D off-lattice stochastic polymerization model to study the subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding and fragmentation of MinD filaments due to MinE. Processivity, protection and fragmentation each reduce stuttering, speed oscillations and MinD filament lengths.

Classification of HIV-1 sequences using profile Hidden Markov Models.

Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain. We show that a standard method that relies on the construction of a positive training set only, to capture unique features associated with a particular subtype, can accurately classify sequences belonging to all subtypes except B and D.

Riboswitch detection using profile hidden Markov models.

Background: Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding.