bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary transitions during RNA virus experimental evolution
Authors: Elena Santiago F. 
Published: July 2016

In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.
This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
The major synthetic evolutionary transitions
Authors: Solé Ricard 
Published: July 2016

Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.
This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Editing of the urease gene by CRISPR-Cas in the diatomThalassiosira pseudonana
Authors: Hopes Amanda , Nekrasov Vladimir , Kamoun Sophien , Mock Thomas 
Published: July 2016

AbstractBackground: CRISPR-Cas is a recent and powerful edition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome ofT. pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas.Results: A single construct wa assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤ 61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate.Conclusions: CRISPR-Cas can precisely and efficiently edit the genome ofT. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.
A Multi-Scale Computational Model of the effects of TMS on Motor Cortex
Authors: Seo Hyeon , Schaworonkow Natalie , Jun Sung Chan , Triesch Jochen 
Published: July 2016

AbstractThe detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different cell types in motor cortex due to transcranial magnetic stimulation. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict detailed neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to predict activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also predicts differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of corctial pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.
The haplotype-resolved genome sequence of hexaploidIpomoea batatasreveals its evolutionary history
Authors: Yang Jun , Moeinzadeh M-Hossein , Kuhl Heiner , Helmuth Johannes , Xiao Peng , Liu Guiling , Zheng Jianli , Sun Zhe , Fan Weijuan , Deng Gaifang , Wang Hongxia , Hu Fenhong , R Fernie Alisdair , Timmermann Bernd , Zhang Peng , Vingron Martin 
Published: July 2016

AbstractAlthough the sweet potato,Ipomoea batatas, is the seventh most important crop in the world and the fourth most significant in China, its genome has not yet been sequenced. The reason, at least in part, is that the genome has proven very difficult to assemble, being hexaploid and highly polymorphic; it has a presumptive composition of two B1and four B2component genomes (B1B1B2B2B2B2). By using a novel haplotyping method based on de novo genome assembly, however, we have produced a half haplotype-resolved genome from ∼267Gb of paired-end sequence reads amounting to roughly 60-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two whole genome duplication events as occurring about 525,000 and 341,000 years ago. Our analysis also identified many clusters of genes for specialized compounds biosynthesis in this genome. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using direct sequencing of the polyploid organism itself rather than of any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.
Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell R packages
Authors: Deveau Paul , Barillot Emmanuel , Boeva Valentina , Zinovyev Andrei , Bonnet Eric 
Published: July 2016

AbstractBiological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, such as the Atlas of Cancer Signaling Network (ACSN). All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe the R packageACSNMineRfor calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSN molecular pathways, but can use any molecular pathway encoded as a GMT file, for instance sets of genes available in the Molecular Signatures Database (MSigDB). We also present the R packageRNaviCell, that can be used in conjunction withACSNMineRto visualize different data types on web-based, interactive ACSN maps. We illustrate the functionalities of the two packages with biological data taken from large-scale cancer datasets.
Strehler-Mildvan correlation is a degenerate manifold of Gompertz fit
Authors: Tarkhov Andrei E. , Menshikov Leonid I. , Fedichev Peter O. 
Published: July 2016

AbstractGompertz empirical law of mortality is often used in practical research to parametrize survival fraction as a function of age with the help of just two quantities: the Initial Mortality Rate (IMR) and the Gompertz exponent, inversely proportional to the Mortality Rate Doubling Time (MRDT). The IMR is often found to be inversely related to the Gompertz exponent, which is the dependence commonly referred to as Strehler-Mildvan (SM) correlation. In this paper, we address fundamental uncertainties of the Gompertz parameters inference from experimental Kaplan-Meier plots and show, that a least squares fit often leads to an ill-defined non-linear optimization problem, which is extremely sensitive to sampling errors and the smallest systematic demographic variations. Therefore, an analysis of consequent repeats of the same experiments in the same biological conditions yields the whole degenerate manifold of possible Gompertz parameters. We find that whenever the average lifespan of species greatly exceeds MRDT, small random variations in the survival records produce large deviations in the identified Gompertz parameters along the line, corresponding to the set of all possible IMR and MRDT values, roughly compatible with the properly determined value of average lifespan in experiment. The best fit parameters in this case turn out to be related by a form of SM correlation. Therefore, we have to conclude that the combined property, such as the average lifespan in the group, rather than IMR and MRDT values separately, may often only be reliably determined via experiments, even in a perfectly homogeneous animal cohort due to its finite size and/or low age-sampling frequency, typical for modern high-throughput settings. We support our findings with careful analysis of experimental survival records obtained in cohorts ofC. elegansof different sizes, in control groups and under the influence of experimental therapies or environmental conditions. We argue that since, SM correlation may show up as a consequence of the fitting degeneracy, its appearance is not limited to homogeneous cohorts. In fact, the problem persists even beyond the simple Gompertz mortality law. We show that the same degeneracy occurs exactly in the same way, if a more advanced Gompertz-Makeham aging model is employed to improve the modeling. We explain how SM type of relation between the demographic parameters may still be observed even in extremely large cohorts with immense statistical power, such as in human census datasets, provided that systematic historical changes are weak in nature and lead to a gradual change in the mean lifespan.
The evolution of genetic bandwagoning
Authors: Solon Idan S. 
Published: July 2016

AbstractBackgroundIn separate literatures, biologists have marshaled theoretical and empirical support for theories that a variant can be selected to (1) induce suicide by moribund or otherwise stressed holders; (2) induce suicide by a holder with low productive or reproductive potential; (3) impose senescence upon a chronologically old holder; and (4) reduce the yield of a holder with low genetic heterozygosity. High stress, moribundity, low productive and reproductive potential, high chronological age, and low genetic heterozygosity all indicate the holder has a relative paucity of advantageous genetic variants in acquiring prey, territory, and mates or surviving predators and parasites. Therefore, an unappreciated commonality between these theories is that a variant can be selected that reduces the fitness of a holder of low genetic quality.Here, I argue that a variant can be selected that reduces its holder’s fitness in response to not just these indications but also other indications of low genetic quality. The fitness losses induced by the variant in low-quality individuals allow fitness gains for nearby individuals, some of which hold a copy of the variant. The variant gains frequency by hitchhiking along with (“jumping on the bandwagon” of) higher-quality individuals (and their lineages) that have copies of the variant; therefore, it is called a “bandwagoning” variant.QuestionsWhat parameter values (e.g., population quantity, relatedness, heritability of reproductive success) allow natural selection of genetic bandwagoning?Features of the modelThe model is an individual-based Moran process. Each individual’s quality value is randomly chosen at birth from a normal distribution that has a mean equal to the quality value of its parent.Ranges of parametersTotal population quantity varied from 50 to 500. Assortment (“relatedness”) in the population varied from .05 to .15. Recorded values for the heritability of reproductive success varied from .024 to .132.ConclusionsNatural selection of genetic bandwagoning can occur even when values for population quantity, relatedness, and heritability of reproductive success are low enough to be in line with reported values for humans and other species. Therefore, genetic bandwagoning theory can explain why indications of an organism’s low genetic quality induce behavior by, or biological processes within, that organism that reduce that organism’s fitness.
The Origin of Coupled Chloride and Proton Transport in a Cl−/H+Antiporter
Authors: Lee Sangyun , Mayes Heather B. , Swanson Jessica M. J. , Voth Gregory A. 
Published: July 2016

AbstractThe ClC family of transmembrane proteins functions throughout nature to control the transport of Cl−ions across biological membranes. ClC-ec1 fromEscherichia coliis an antiporter, coupling the transport of Cl−and H+ions in opposite directions and driven by the concentration gradients of the ions. Despite keen interest in this protein, the molecular mechanism of the Cl−/H+coupling has not been fully elucidated. Here, we have used multiscale simulation to help identify the essential mechanism of the Cl−/H+coupling. We find that the highest barrier for proton transport (PT) from the intra- to extracellular solution is attributable to a chemical reaction—the deprotonation of glutamic acid 148 (E148). This barrier is significantly reduced by the binding of Cl−in the “central” site (Cl−cen), which displaces E148 and thereby facilitates its deprotonation. Conversely, in the absence of Cl−cenE148 favors the “down” conformation, which results in a much higher cumulative rotation and deprotonation barrier that effectively blocks PT to the extracellular solution. Thus, the rotation of E148 plays a critical role in defining the Cl−/H+coupling. As a control, we have also simulated PT in the ClC-ec1 E148A mutant to further understand the role of this residue. Replacement with a non-protonatable residue greatly increases the free energy barrier for PT from E203 to the extracellular solution, explaining the experimental result that PT in E148A is blocked whether or not Cl−cenis present. The results presented here suggest both how a chemical reaction can control the rate of PT and also how it can provide a mechanism for a coupling of the two ion transport processes.
Balance between resource supply and demand determines nutrient limitation of primary productivity in the ocean
Authors: Hagstrom George I. , Levin Simon A. , Martiny Adam C. 
Published: July 2016

AbstractWhat is the ultimate limiting nutrient in the ocean? The dominant theory, which was first proposed by Redfield and later formalized by Tyrrell[1, 2], states that despite the scarcity of fixed nitrogen (N) in the surface ocean, phosphorus (P) availability ultimately determines primary productivity. Two recent findings directly challenge the assumptions of the Redfield-Tyrrell paradigm: the discovery of systematic variations of phytoplankton cellular N:P:Fe and widespread iron-limitation of phytoplankton. Here we use a simple model of nitrogen, phosphorus, and iron (Fe) cycling to show how the resource demand ratios and biogeography of phytoplankton interact with external resource supply ratios to govern nutrient cycling and primary productivity. We find that all three nutrients can limit global primary productivity, and that the ratio of geochemical supply to biological demand of each nutrient in each ocean region determines the limiting nutrients, with nitrogen N fixation providing a mechanism for the cycles to interact. These results have important consequences for our understanding of biogeochemical cycles, ocean-atmosphere interactions, marine ecology, and the response of ocean ecosystems to climate change. Our work demonstrates the importance of resource ratios and suggests that future studies of the physiological and geochemical regulation of these ratios are indispensable to building accurate theories and future predictions of nutrient cycling and primary productivity.
Audit quality differences amongst audit firms in a developing economy
Authors: Kaawaase Twaha K. , Assad Mussa Juma , Kitindi Ernest G , Nkundabanyanga Stephen Korutaro 
Published: July 2016

Purpose– The purpose of this paper is to report findings of audit quality differences amongst audit firms in a developing country. Specifically, the authors examine the assumption of marked audit quality differences amongst large audit firms (Big 4s) and the small and medium practices (SMPs).Design/methodology/approach– First, the authors develop scales for assessing perceived audit quality in the financial services sector based on qualitative data obtained from 106 audit practitioners, 31 credit analysts and 13 board members. The authors use NVivo© to analyse the 13 transcribed interviews and follow “cross-case analysis” to visualize dimensions and scales of audit quality. Then the authors use measurement scales developed and obtain quantitative data from 183 board members and top executives in the financial services sector and test for perceived audit quality differences amongst audit firms using a Mann-WhitneyUtest.Findings– The findings suggest that audit quality is a multi-dimensional construct comprising of levels of discretionary accruals; compliance of audited accounts to accounting standards, law and regulations; and audit fees. Based on these measures, the authors find that Big 4 audit firms ensure more compliance with accounting standards, law and other regulatory requirements than SMPs. However, taking all the three audit quality dimensions together reveals no significant differences in audit quality levels between Big 4 and SMPs.Research limitations/implications– In terms of auditor selection and retention, it is important that audit firms are assessed based on their ability to constrain discretionary accruals, to produce audited accounts that comply with requirements of accounting standards, the law and regulations; and to examine the fees they charge in relation to quality of service, than on their size. Also, as the results of this study suggest that Big 4 audit firms might be needed for compliance with accounting standards, law and other regulatory requirements, their audit ties in with the most basic level of auditing requiring probity and legality which, in practice, requires a low level of judgement to be exercised by those performing the audit. It might be useful for Big 4 and other audit firms to embark also on higher level of auditing requiring higher level of judgement. Future research may wish to examine auditing firms’ proclivity to higher level judgment audit.Originality/value– Previous research reveals no consistent way of measuring audit quality and has been inconclusive on the subject of audit quality differential amongst audit firms. The authors create audit quality scales which can be used in assessing perceived audit quality in a developing country context and provide initial evidence of no significant differences between large audit firms and the SMPs regarding audit quality in Uganda.
The stock market’s reaction to accounting information: the cases of Chile and Peru
Authors: Melgarejo Mauricio , Montiel Eduardo , Sanz Luis 
Published: July 2016

Purpose
– The purpose of this paper is to analyze the stock price and volume reactions around firms’ earnings announcement dates in two Latin American stock markets: Chile and Peru.

Design/methodology/approach
– This study uses multivariate regression analysis to determine the impact of accounting information on stock prices and volume traded around the firms’ earnings announcement dates.

Findings
– The authors find that quarterly earnings surprises explain stock abnormal returns and abnormal trading volumes around the earnings announcement dates in the Santiago (Chile) and Lima (Peru) stock exchanges. The authors also find that these two effects are driven by small firms.

Originality/value
– This is one of the first articles to study the price and volume reactions to accounting information in Latin American stock markets.
The insurance agents’ intention to make inappropriate product recommendations
Authors: Tseng Lu-Ming , Kang Yue-Min , Chung Chi-Erh 
Published: July 2016

Purpose
This case study aim to investigate the impacts of insurance agents’ positive attitude toward inappropriate product recommendations on the insurance agents’ intention to make the inappropriate product recommendations. This study further checks how the attitude and intention could be enhanced by the insurer’s manipulation of sales compensations, the agents’ perception of information asymmetry between customers and insurance agents and the insurer’s sales orientation.

Design/methodology/approach
Full-time insurance agents from the life insurance industry in Taiwan were surveyed. To test the hypotheses, hierarchical regression analyses were used in the study.

Findings
The main results showed that the respondents’ positive attitude toward inappropriate product recommendations was the influential predictor of the respondents’ behavioral intention. Nevertheless, the positive attitude was enhanced by the manipulation of sales compensations and the insurer’s sales orientation.

Originality/value
Very few studies have investigated the relationships among information asymmetry between customers and agents, management’s sales orientation, management’s manipulation of sales compensations and the problems of selling unsuitable insurance products to customers. This study may contribute to the relevant literature by discussing these issues.