Study on Phylogenetic Relationships, Variability, and Correlated Mutations in M2 Proteins of Influenza Virus A

M2 channel, an influenza virus transmembrane protein, serves as an important target for antiviral drug design. There are still discordances concerning the role of some residues involved in proton transfer as well as the mechanism of inhibition by commercial drugs. The viral M2 proteins show high conservativity; about 3/4 of the positions are occupied by one residue in over 95%. Nine M2 proteins from the H3N2 strain and possibly two proteins from H2N2 strains make a phylogenic cluster closely related to 2RLF. The variability range is limited to 4 residues/position with one exception. The 2RLF protein stands out by the presence of 2 serines at the positions 19 and 50, which are in most other M2 proteins occupied by cysteines. The study of correlated mutations shows that there are several positions with significant mutational correlation that have not been described so far as functionally important. That there are 5 more residues potentially involved in the M2 mechanism of action. The original software used in this work (Consensus Constructor, SSSSg, Corm, Talana) is freely accessible as stand-alone offline applications upon request to the authors. The other software used in this work is freely available online for noncommercial purposes at public services on bioinformatics such as ExPASy or NCBI. The study on mutational variability, evolutionary relationship, and correlated mutation presented in this paper is a potential way to explain more completely the role of significant factors in proton channel action and to clarify the inhibition mechanism by specific drugs

Hierarchical dynamics of individual RNA helix base pair formation and disruption

This thesis explores the RNA folding problem using single-molecule field effect transistors (smFETs) to measure the lifetimes of individual RNA base-pairing rearrangements. In the course of this research, considerable computational, chemical, and engineering contributions were developed so that the single-molecule measurements could be conducted and quantified. These advancements have allowed, on the basis of the smFET data collected herein, the quantification of a kinetic model for RNA stem-loop structures which has been generalized to quantitatively explore the phenomenological observation that an RNA found in the bacillus subtilis strain acts as a metabolite-sensing switch, allowing RNA polymerase to transcribe the messenger RNA when the metabolite is present and preventing transcription when the metabolite is absent. Together, the data presented quantify a simple model for the base pairing rearrangements that underlie RNA folding

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Task Allocation in Foraging Robot Swarms:The Role of Information Sharing

Autonomous task allocation is a desirable feature of robot swarms that collect and deliver items in scenarios where congestion, caused by accumulated items or robots, can temporarily interfere with swarm behaviour. In such settings, self-regulation of workforce can prevent unnecessary energy consumption. We explore two types of self-regulation: non-social, where robots become idle upon experiencing congestion, and social, where robots broadcast information about congestion to their team mates in order to socially inhibit foraging. We show that while both types of self-regulation can lead to improved energy efficiency and increase the amount of resource collected, the speed with which information about congestion flows through a swarm affects the scalability of these algorithms

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance

Patterns of Foraminiferal Micro-evolution and Enviromental Change in the Lower Chalk

The research tests Sheldon's Plus ҫa change model by tracking a single fossil lineage through a succession of marine environments showing geological-scale differences in background stability. Orbitally driven cyclic sediments of Cenomanian age, predominantly recording a 20 kyr precessional shift, provide both the time-frame and the main engine of environmental variability, although transgressive pulses and other events are also superimposed. The cyclicity provides spectacular geographical and temporal control,, allowing a million-year sequence to be sampled at 100 kyr intervals at three laterally adjacent sites, and partially sampled at 20 kyr and 2 kyr intervals at one of these sites. The lineage of interest is a benthic agglutinated foraminiferan, Tritaxia pyramidata, which occurs in prolific numbers; additional ecological evidence comes from a large microfossil database recovered from the same samples. The Lower Chalk benthic microfauna have very stable patterns of relative abundance, with the same species occurring in similar proportions for at least a million years. Analysis of Tritaxia's ecology identifies it as an r-selected generalist playing a keystone role in the community. During development, Tritaxia exhibits a persistent tendency to uncoil, but this tendency is strongly manifest only after average life expectancy, leading to its interpretation as a construction mistake rather than a product of design. This developmental quirk sheds light on the grain and texture of the morphospace through which Tritaxia is forced to navigate, significantly limiting its evolutionary potential. The result is a lineage that achieves a million years' worth of wobbly stasis, largely because it is boxed into a small corner of morphospace by the joint influence of a narrow developmental channel and competitive interference from other species. The dynamics, of this process predominantly support the Plus ҫa change model, even though not all the predicted patterns are found