Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174

<p>Abstract</p> <p>Background</p> <p>In large asexual populations where beneficial mutations may co-occur and recombination is absent, the fate of beneficial mutations can be significantly affected by competition (i.e., clonal interference). Theoretical models predict that clonal interference (CI) can slow adaptation, alter the distribution of fixed beneficial mutations, and affect disease progression by impacting within-host evolution of pathogens. While phenotypic data support that CI is a significant determinant of adaptive outcome, genetic data are needed to verify the patterns and to inform evolutionary models. We adapted replicate populations of the bacteriophage φX174 under two levels of CaCl₂to create benign and harsh environments. Genomic sequences of multiple individuals from evolved populations were used to detect competing beneficial mutations.</p> <p>Results</p> <p>There were several competing genotypes in most of the populations where CaCl₂was abundant, but no evidence of CI where CaCl₂was scarce, even though rates of adaptation and population sizes among the treatments were similar. The sequence data revealed that observed mutations were limited to a single portion of one gene in the harsh treatment, but spanned a different and larger region of the genome under the benign treatments, suggesting that there were more adaptive solutions to the benign treatment.</p> <p>Conclusion</p> <p>Beneficial mutations with relatively large selection coefficients can be excluded by CI. CI may commonly determine the fate of beneficial mutations in large microbial populations, but its occurrence depends on selective conditions. CI was more frequent in benign selective conditions possibly due to a greater number of adaptive targets under this treatment. Additionally, the genomic sequence data showed that selection can target different types and numbers of phenotypes in environments that differ by only a single continuous variable.</p

LI cancellation and power allocation for multipair FD relay systems with massive antenna arrays

Massive antenna arrays are capable of cancelling out the loop interference (LI) at the relay station in multipair full-duplex (FD) relay networks even without LI channel knowledge if the number of antennas is allowed to grow without a bound. For large but finite number of antennas, however, channel estimation based LI cancellation is required. In this paper, we propose a pilot protocol for LI channel estimation by exploiting the channel coherence time difference between static and moving transceivers in a multipair FD relay system. To maximize the end-to-end achievable rate, we also design a novel power allocation scheme to adjust the transmit power of each link at the relay. The analytical and numerical results show that the proposed novel pilot protocol and power allocation scheme jointly improve spectral and energy efficiency significantly with realistic coherence time differences

Index Modulation-based Information Harvesting for Far-Field RF Power Transfer

While wireless information transmission (WIT) is evolving into its sixth generation (6G), maintaining terminal operations that rely on limited battery capacities has become one of the most paramount challenges for Internet-of-Things (IoT) platforms. In this respect, there exists a growing interest in energy harvesting technology from ambient resources, and wireless power transfer (WPT) can be the key solution towards enabling battery-less infrastructures referred to as zero-power communication technology. Indeed, eclectic integration approaches between WPT and WIT mechanisms are becoming a vital necessity to limit the need for replacing batteries. Beyond the conventional separation between data and power components of the emitted waveforms, as in simultaneous wireless information and power transfer (SWIPT) mechanisms, a novel protocol referred to as information harvesting (IH) has recently emerged. IH leverages existing WPT mechanisms for data communication by incorporating index modulation (IM) techniques on top of the existing far-field power transfer mechanism. In this paper, a unified framework for the IM-based IH mechanisms has been presented where the feasibility of various IM techniques are evaluated based on different performance metrics. The presented results demonstrate the substantial potential to enable data communication within existing far-field WPT systems, particularly in the context of next-generation IoT wireless networks.Comment: 13 pages, 9 figure

Comparing Electronic Monitoring and human observer collected fishery data in the tropical purse seine operating in the Western and Central Pacific Ocean

Electronic Monitory (EM) systems have been proven a valid tool for collecting fishery dependent data. They are being widely used in many fisheries as a complement or alternative to human observers to increase the monitoring coverage of fisheries. However, considering its wide application, following agreed minimum standard, it is important to compare the congruence between the information collected by EM and observers. We compared EM and two sets of different observer data collected on 6 trips of tuna purse seiners in the Eastern and Western and Central Pacific Ocean to analyze the similarity of fishing set type identification, estimation of tuna and bycatch catches between both monitoring systems. Overall EM was a valid tool to estimate the type of fishing set. Retained total catch of tunas by set was estimated by EM as reliable as that by both observer programs and logbook. When comparing the information by set, EM estimation of the main species, such as skipjack and bigeye and the combination of bigeye/yellowfin, was proven to be less accurate but statistically similar to the estimates made by both observers’ programs. EM tended to underestimate the retained catch of skipjack in comparison to both observers estimates and slightly overestimate bigeye and yellowfin, the overestimation being less pronounced for bigeye than for yellowfin. For bycatch species, EM is able to identify main bycatch species as observers do. However, the capability of EM to estimate the same number of bycatch items in comparison to IATTC and WCPFC observers varies greatly by species group. For sharks, which are the main bycatch issue in the FAD purse seine fishery, the overall congruence between EM and observers was high. EM and IATTC observer identified a similar overall number of individual sharks, however, WCPFC observers estimated lower number of shark individuals than the other two monitoring systems when considering all trips together.Versión del edito

Creep and Creep-Fatigue Crack Growth at Structural Discontinuities and Welds

The subsection ASME NH high temperature design procedure does not admit crack-like defects into the structural components. The US NRC identified the lack of treatment of crack growth within NH as a limitation of the code and thus this effort was undertaken. This effort is broken into two parts. Part 1, summarized here, involved examining all high temperature creep-fatigue crack growth codes being used today and from these, the task objective was to choose a methodology that is appropriate for possible implementation within NH. The second part of this task, which has just started, is to develop design rules for possible implementation within NH. This second part is a challenge since all codes require step-by-step analysis procedures to be undertaken in order to assess the crack growth and life of the component. Simple rules for design do not exist in any code at present. The codes examined in this effort included R5, RCC-MR (A16), BS 7910, API 579, and ATK (and some lesser known codes). There are several reasons that the capability for assessing cracks in high temperature nuclear components is desirable. These include: (1) Some components that are part of GEN IV reactors may have geometries that have sharp corners - which are essentially cracks. Design of these components within the traditional ASME NH procedure is quite challenging. It is natural to ensure adequate life design by modeling these features as cracks within a creep-fatigue crack growth procedure. (2) Workmanship flaws in welds sometimes occur and are accepted in some ASME code sections. It can be convenient to consider these as flaws when making a design life assessment. (3) Non-destructive Evaluation (NDE) and inspection methods after fabrication are limited in the size of the crack or flaw that can be detected. It is often convenient to perform a life assessment using a flaw of a size that represents the maximum size that can elude detection. (4) Flaws that are observed using in-service detection methods often need to be addressed as plants age. Shutdown inspection intervals can only be designed using creep and creep-fatigue crack growth techniques. (5) The use of crack growth procedures can aid in examining the seriousness of creep damage in structural components. How cracks grow can be used to assess margins on components and lead to further safe operation. After examining the pros and cons of all these methods, the R5 code was chosen as the most up-to-date and validated high temperature creep and creep fatigue code currently used in the world at present. R5 is considered the leader because the code: (1) has well established and validated rules, (2) has a team of experts continually improving and updating it, (3) has software that can be used by designers, (4) extensive validation in many parts with available data from BE resources as well as input from Imperial college's database, and (5) was specifically developed for use in nuclear plants. R5 was specifically developed for use in gas cooled nuclear reactors which operate in the UK and much of the experience is based on materials and temperatures which are experienced in these reactors. If the next generation advanced reactors to be built in the US used these same materials within the same temperature ranges as these reactors, then R5 may be appropriate for consideration of direct implementation within ASME code NH or Section XI. However, until more verification and validation of these creep/fatigue crack growth rules for the specific materials and temperatures to be used in the GEN IV reactors is complete, ASME should consider delaying this implementation. With this in mind, it is this authors opinion that R5 methods are the best available for code use today. The focus of this work was to examine the literature for creep and creep-fatigue crack growth procedures that are well established in codes in other countries and choose a procedure to consider implementation into ASME NH. It is very important to recognize that all creep and creep fatigue crack growth procedures that are part of high temperature design codes are related and very similar. This effort made no attempt to develop a new creep-fatigue crack growth predictive methodology. Rather examination of current procedures was the only goal. The uncertainties in the R5 crack growth methods and recommendations for more work are summarized here also

The Genetics of Adaptation for Eight Microvirid Bacteriophages

Theories of adaptive molecular evolution have recently experienced significant expansion, and their predictions and assumptions have begun to be subjected to rigorous empirical testing. However, these theories focus largely on predicting the first event in adaptive evolution, the fixation of a single beneficial mutation. To address long-term adaptation it is necessary to include new assumptions, but empirical data are needed for guidance. To empirically characterize the general properties of adaptive walks, eight recently isolated relatives of the single-stranded DNA (ssDNA) bacteriophage φX174 (family Microviridae) were adapted to identical selective conditions. Three of the eight genotypes were adapted in replicate, for a total of 11 adaptive walks. We measured fitness improvement and identified the genetic changes underlying the observed adaptation. Nearly all phages were evolvable; nine of the 11 lineages showed a significant increase in fitness. However, fitness plateaued quickly, and adaptation was achieved through only three substitutions on average. Parallel evolution was rampant, both across replicates of the same genotype as well as across different genotypes, yet adaptation of replicates never proceeded through the exact same set of mutations. Despite this, final fitnesses did not vary significantly among replicates. Final fitnesses did vary significantly across genotypes but not across phylogenetic groupings of genotypes. A positive correlation was found between the number of substitutions in an adaptive walk and the magnitude of fitness improvement, but no correlation was found between starting and ending fitness. These results provide an empirical framework for future adaptation theory

Experimental evolution of viruses: Microviridae as a model system

φX174 was developed as a model system for experimental studies of evolution because of its small genome size and ease of cultivation. It has been used extensively to address statistical questions about the dynamics of adaptive evolution. Molecular changes seen during experimental evolution of φX174 under a variety of conditions were compiled from 10 experiments comprising 58 lineages, where whole genomes were sequenced. A total of 667 substitutions was seen. Parallel evolution was rampant, with over 50 per cent of substitutions occurring at sites with three or more events. Comparisons of experimentally evolved sites to variation seen among wild phage suggest that at least some of the adaptive mechanisms seen in the laboratory are relevant to adaptation in nature. Elucidation of these mechanisms is aided by the availability of capsid and pro-capsid structures for φX174 and builds on years of genetic studies of the phage life history