Search

Aureochromes are unique blue light-responsive LOV (Light Oxygen Voltage) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in this brown photosynthetic algae. Both the LOV sensor and the bZIP effector shows overall sequence-structure conservation. The structurally similar LOV+bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles – though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and, information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.

Networks with a scale-free degree distribution are widely thought to promote cooperation in various games. Herein, by studying the well-known prisoner's dilemma game, we demonstrate that this need not necessarily be true. For the very same degree sequence and degree distribution, we present a variety of possible behaviour. We reassess the perceived importance of hubs in a network towards the maintenance of cooperation. We also reevaluate the dependence of cooperation on network clustering and assortativity., Accepted to Europhysics Letters (EPL)

The detection and management of diseases become quite complicated when pathogens contain asymptomatic phenotypes amongst their ranks, as evident during the recent COVID-19 pandemic. Spreading of diseases has been studied extensively under the paradigm of Susceptible - Infected - Recovered - Deceased (SIRD) dynamics. Various game-theoretic approaches have also addressed disease spread, many of which consider S, I, R, and D as strategies rather than as states. Remarkably, most studies from the above approaches do not account for the distinction between the symptomatic or asymptomatic aspect of the disease. It is well-known that precautionary measures like washing hands, wearing masks and social distancing significantly mitigate the spread of many contagious diseases. Herein, we consider the adoption of such precautions as strategies and treat S, I, R, and D as states. We also attempt to capture the differences in epidemic spreading arising from symptomatic and asymptomatic diseases on various network topologies. Through extensive computer simulations, we examine that the cost of maintaining precautionary measures as well as the extent of mass testing in a population affects the final fraction of socially responsible individuals. We observe that the lack of mass testing could potentially lead to a pandemic in case of asymptomatic diseases. Network topology also seems to play an important role. We further observe that the final fraction of proactive individuals depends on the initial fraction of both infected as well as proactive individuals. Additionally, edge density can significantly influence the overall outcome. Our findings are in broad agreement with the lessons learnt from the ongoing COVID-19 pandemic., To appear in the special issue on "Emerging trends in modeling and analysis of complex systems" of Journal of the Indian Institute of Science (J IISc) (2021)

The maintenance of cooperation in the presence of spatial restrictions has been studied extensively. It is well-established that the underlying graph topology can significantly influence the outcome of games on graphs. Maintenance of cooperation could be difficult, especially in the absence of spatial restrictions. The evolution of cooperation would naturally depend on payoffs. However, payoffs are generally considered to be invariant in a given game. A natural yet unexplored question is whether the topology of the underlying structures on which the games are played, possesses no role whatsoever in the determination of payoffs. Herein, we introduce the notion of cooperator graphs and defector graphs as well as a new form of game payoff, which is weakly dependent on the underlying network topology. These concepts are inspired by the well-known microbial phenomenon of quorum sensing. We demonstrate that even with such a weak dependence, the fundamental game dynamics and indeed the very nature of the game may be altered. Such changes in the nature of a game have been well-reported in theoretical and experimental studies., Comment: Replaced by the version accepted to European Physical Journal B