bluuebunny/crossref_metadata_2025_split huggingface dataset:
After the games are over: life-history trade-offs drive dispersal attenuation following range expansion
Authors: Alex Perkins T. , Boettiger Carl , Phillips Benjamin L. 
Published: February 2015

ABSTRACTIncreased dispersal propensity often evolves on expanding range edges due to the Olympic Village effect, which involves the fastest and fittest finding themselves together in the same place at the same time, mating, and giving rise to like individuals. But what happens after the range’s leading edge has passed and the games are over? Although empirical studies indicate that dispersal propensity attenuates following range expansion, hypotheses about the mechanisms driving this attenuation have not been clearly articulated or tested. Here we use a simple model of the spatiotemporal dynamics of two phenotypes, one fast and the other slow, to propose that dispersal attenuation beyond pre-expansion levels is only possible in the presence of trade-offs between dispersal and life-history traits. The Olympic Village effect ensures that fast dispersers pre-empt locations far from the range’s previous limits. When trade-offs are absent, this pre-emptive spatial advantage has a lasting impact, with highly dispersive individuals attaining equilibrium frequencies that are strictly higher than their introduction frequencies. When trade-offs are present, dispersal propensity decays rapidly at all locations. Our model’s results about the post-colonization trajectory of dispersal evolution are clear and, in principle, should be observable in field studies. We conclude that empirical observations of post-colonization dispersal attenuation offer a novel way to detect the existence of otherwise elusive trade-offs between dispersal and life-history traits.
Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors
Authors: Radó-Trilla Núria , Arató Krisztina , Pegueroles Cinta , Raya Alicia , de la Luna Susana , Albà M.Mar 
Published: February 2015

AbstractThe high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families (107 out of 237) originated during the 2R-WGD contain LCRs, compared to only a small percentage of the non-duplicated TF genes used as a control (15 out of 115). At the individual gene level, we observe that twice as many duplicated TFs have gained LCRs as non-duplicated TFs. In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
Authors: Mariotti Marco , Santesmasses Didac , Capella-Gutierrez Salvador , Mateo Andrea , Arnan Carme , Johnson Rory , D’Aniello Salvatore , Yim Sun Hee , Gladyshev Vadim N , Serras Florenci , Corominas Montserrat , Gabaldón Toni , Guigé Roderic 
Published: February 2015

AbstractSPS catalyzes the synthesis of selenophosphate, the selenium donor for the synthesis of the amino acid selenocysteine (Sec), incorporated in selenoproteins in response to the UGA codon. SPS is unique among proteins of the selenoprotein biosynthesis machinery in that it is, in many species, a selenoprotein itself, although, as in all selenoproteins, Sec is often replaced by cysteine (Cys). In metazoan genomes we found, however, SPS genes with lineage specific substitutions other than Sec or Cys. Our results show that these non-Sec, non-Cys SPS genes originated through a number of independent gene duplications of diverse molecular origin from an ancestral selenoprotein SPS gene. Although of independent origin, complementation assays in fly mutants show that these genes share a common function, which most likely emerged in the ancestral metazoan gene. This function appears to be unrelated to selenophosphate synthesis, since all genomes encoding selenoproteins contain Sec or Cys SPS genes (SPS2), but those containing only non-Sec, non-Cys SPS genes (SPS1) do not encode selenoproteins. Thus, in SPS genes, through parallel duplications and subsequent convergent subfunctionalization, two functions initially carried by a single gene are recurrently segregated at two different loci. RNA structures enhancing the readthrough of the Sec-UGA codon in SPS genes, which may be traced back to prokaryotes, played a key role in this process. The SPS evolutionary history in metazoans constitute a remarkable example of the emergence and evolution of gene function. We have been able to trace this history with unusual detail thanks to the singular feature of SPS genes, wherein the amino acid at a single site determines protein function, and, ultimately, the evolutionary fate of an entire class of genes.
Linkage Disequilibrium and Inversion-Typing of theDrosophila melanogasterGenome Reference Panel
Authors: Houle David , Márquez Eladio J. 
Published: February 2015

ABSTRACTWe calculated the linkage disequilibrium between all pairs of variants in the Drosophila Genome Reference Panel with minor allele count equal to or greater than 5. We usedr2≥0.5 as the cutoff for a highly correlated SNP. We make available the list of all highly correlated SNPs for use in association studies. Seventy-six percent of variant SNPs are highly correlated with at least one other SNP, and the mean number of highly correlated SNPs per variant over the whole genome is 83.9. Disequilibrium between distant SNPs is also common when minor allele frequency (MAF) is low: 37% of SNPs with MAF<0.1 are highly correlated with SNPs more than 100kb distant. While SNPs within regions with polymorphic inversions are highly correlated with somewhat larger numbers of SNPs, and these correlated SNPs are on average farther away, the probability that a SNP in such regions is highly correlated with at least one other SNP is very similar to SNPs outside inversions. Previous karyotyping of the DGRP lines has been inconsistent, and we used LD and genotype to investigate these discrepancies. When previous studies agreed on inversion karyotype, our analysis was almost perfectly concordant with those assignments. In discordant cases, and for inversion heterozygotes, our results suggest errors in two previous analyses, or discordance between genotype and karyotype. Heterozygosities of chromosome arms are in many cases surprisingly highly correlated, suggesting strong epsistatic selection during the inbreeding and maintenance of the DGRP lines.
Methodology for acquisition of collective tacit knowledge used in diagnosis of defect cause in industrial processes
Authors: Rosário Cláudio Roberto , Kipper Liane Mahlmann , Frozza Rejane , Mariani Bruna Bueno 
Published: February 2015

Purpose
– The purpose of this paper was to build the MACTAK methodology, which aims to transform collective tacit knowledge into the explicit one using knowledge elicitation techniques, associated to quality tools structured by systemography, represent it in a symbolic language and production rules and model it in two expert systems which can assist the investigation of defect causes during the metal packaging production process.

Design/methodology/approach
– The method applied in the research was classified as exploratory, because a preliminary study was conducted, to better suit the mapping methodology for eliciting collective tacit knowledge, to the reality which was intended to be known. Through studies and the application of the systemography technique, a methodology for the elicitation of collective tacit knowledge has been developed. It suggests a systematic sequence of activities, to map and transform collective tacit knowledge into the explicit one, on the production process which was studied.

Findings
– The types of tacit knowledge were mapped and became explicit through the application of the methodology proposed. A knowledge management system was created, as such knowledge was validated by other mechanics during their training on the shop-floor, which resulted in a structure of unique and shared knowledge. They became explicit for being stored in a knowledge base and presented to its users through the expert system. It is concluded that the methodology of acquiring collective tacit knowledge helped on the reduction of rework index by standardizing the way used to investigate the cause of the defect, in the studied company.

Research limitations/implications
– The MACTAK methodology was developed for exclusive use in industrial processes where the following elements are presented: process, method, environment, raw materials, labor work, measurement and machine. In this method, the detection of the problem occurs from statistical data.

Practical implications
– The methodology began in August 2010, and in October 2011, obtained as a result a reduction in rework cost equivalent to US$17,780.95.

Originality/value
– The methodology is unique, as it refers to the systematic use of knowledge acquisition techniques and tools of quality, and the methodology has a characteristic of direct application in manufacturing processes. The beneficiaries, in this case, are mechanicals of production and quality inspectors that work at the operation level in the company. For the organizational and tactical level, the beneficiaries are engineers of production.
Using essential processes in knowledge integration for knowledge enhancement
Authors: Mohd. Rodzi Mohd. Zuhaili , Ahmad Mohammad Nazir , Zakaria Nor Hidayati 
Published: February 2015

Purpose– This paper aims to study the significant role of knowledge integration, which has a considerable influence on the growth of civilisation and modernisation. It identifies the essential processes in knowledge integration for establishing common understanding, thus enabling long-term sustainability in a dynamic environment that requires continuous adaptability. By understanding the essential processes of knowledge integration, the timely creation of new knowledge is ensured as a solution for critical problems; thus enhancing past and present knowledge.Design/methodology/approach– The paper undertakes a comparative analysis of research in the literature on knowledge integration and derives the essential processes in knowledge integration from existing theories.Findings– Generally, there are various interpretations of knowledge integration that complicate the understanding and implementation of knowledge integration in many organisations. This study extracts the implicit nature of knowledge integration by explicitly proposing its essential processes, namely: identification, creation, assimilation and evaluationto identify the core elements necessary for any initiative in knowledge integration.Research limitations/implications– A number of barriers and dependencies exist in knowledge integration. These are categorised as individual, structural and ontological factors.Practical implications– The utilisation of the essential processes of knowledge integration increases the speed of knowledge creation through the elimination of redundant conventional processes. This indirectly establishes a generic form of knowledge integration, allowing effective communication among knowledge practitioners.Originality/value– The paper’s originality lies in the explicit proposal of the essential processes of knowledge integration, referred to as identification, creation, assimilation and evaluation. Furthermore, this paper highlights the potential of essential processes to act as an ontology that can bridge the real and virtual world of knowledge integration implementation through a generic understanding of the knowledge integration concept among practitioners.
Enhancement of the immunogenicity of a porcine circovirus type 2 DNA vaccine by a recombinant plasmid coexpressing capsid protein and porcine interleukin‐6 in mice
Authors: Guo Xiao‐Qing , Wang Lin‐Qing , Qiao Han , Yang Xing‐Wu , Yang Ming‐Fan , Chen Hong‐Ying 
Published: February 2015

ABSTRACTThe development of effective vaccines against porcine circovirus type 2 (PCV2) has been accepted as an important strategy in the prophylaxis of post‐weaning multisystemic wasting syndrome; a DNA vaccine expressing the major immunogenic capsid (Cap) protein of PCV2 is considered to be a promising candidate. However, DNA vaccines usually induce weak immune responses. In this study, it was found that the efficacy of a DNA vaccine expressing Cap protein was improved by simultaneous expression of porcine IL‐6. A plasmid (pIRES‐ORF2/IL6) separately expressing both Cap protein and porcine IL‐6 was constructed and compared with another plasmid (pIRES‐ORF2) expressing Cap protein for its potential to induce PCV2‐specific immune responses. Mice were vaccinated i.m. twice at 3 week intervals and the induced humoral and cellular responses evaluated. All animals vaccinated with pIRES‐ORF2/IL6 and pIRES‐ORF2 developed specific anti‐PCV2 antibodies (according to enzyme‐linked immunosorbent assay) and a T lymphocyte proliferation response. The percentages of CD3+, CD3+CD8+, and CD3+CD4+ subgroups of peripheral blood T‐lymphocytes were significantly higher in mice immunized with pIRES‐ORF2/IL6 than in those that had received pIRES‐ORF2. After challenge with the virulent PCV2 Wuzhi isolate, mice vaccinated with pIRES‐ORF2/IL6 had significantly less viral replication than those vaccinated with pIRES‐ORF2, suggesting that the protective immunity induced by pIRES‐ORF2/IL6 is superior to that induced by pIRES‐ORF2.
Mannan‐binding lectin reduces CpG DNA‐induced inflammatory cytokine production by human monocytes
Authors: Tang Yuan , Ma Di , Ming Siqi , Zhang Liyun , Zhou Jia , Shan Guiqiu , Chen Zhengliang , Lu Xiao , Zuo Daming 
Published: February 2015

ABSTRACTMannan‐binding lectin (MBL) belongs to the collectin family and functions as an opsonin that can also initiate complement activation. Our previous study showed that MBL serves as a double‐stranded RNA binding protein that attenuates polyriboinosinic‐polyribocytidylic acid‐induced TLR3 activation. Prompted by these findings, in the present study cross‐talk between MBL and CpG‐DNA‐induced TLR9 activation was investigated. Here, it was found that MBL also interacts with the TLR9 agonist, CpG oligodeoxynucleotide (CpG‐ODN), in a calcium‐dependent manner. Purified MBL protein suppressed activation of nuclear factor‐kappa B signaling and subsequent production of proinflammatory cytokines from human monocytes induced by CpG‐ODN 2006. These observations indicate that MBL can down‐regulate CpG DNA‐induced TLR9 activation, emphasizing the importance of understanding the interaction of MBL with TLR agonist in host immune defense.
Trade‐offs between transgenerational transfer of nutritional stress tolerance and immune priming
Authors: Shikano Ikkei , Oak Miranda C. , Halpert‐Scanderbeg Olivia , Cory Jenny S. 
Published: February 2015

Summary

Transgenerational effects are often assumed to have adaptive value as a driver of variation in offspring and parental fitness. Studies of transgenerational effects often focus on single environmental variables. However, in nature, it is unlikely for one factor to vary independently from others and there are likely to be trade‐offs between different stressors.

We altered the nutritional environment of both parents and offspring to examine how nutritional stress influences transgenerational immune priming (TGIP) with a sublethal challenge by the bacterial pathogen Bacillus thuringiensis, in the cabbage looper, Trichoplusia ni.

Transgenerational immune priming was adaptive when offspring encountered the same pathogen experienced by their parents, such that offspring resistance to B. thuringiensis increased 1·5‐fold and antibacterial activity in the haemolymph increased by as much as 4‐fold. However, this was not a general increase in pathogen resistance as susceptibility to a second pathogen, the baculovirus, TnSNPV remained the same. Interestingly, nutritional stress in the parents both enhanced nutritional stress tolerance of offspring and heightened resistance to both B. thuringiensis and TnSNPV. Elevated pathogen resistance was linked to increased egg size.

There was a significant trade‐off between TGIP and the transfer of nutritional stress tolerance when parents encountered both stressors simultaneously, such that parents transferred resistance to pathogens but not nutritional stress tolerance.

These results highlight the trade‐offs that can modulate the occurrence and magnitude of transgenerational effects and illustrate the importance of assessing interactions between multiple environmental variables. At high population densities, disease risk increases and resour‐ces become depleted. Thus, our findings could have significant implications for population dynamics.
Host age modulates parasite infectivity, virulence and reproduction
Authors: Izhar Rony , Ben‐Ami Frida 
Published: February 2015

Summary

Host age is one of the most striking differences among hosts within most populations, but there is very little data on how age‐dependent effects impact ecological and evolutionary dynamics of both the host and the parasite.

Here, we examined the influence of host age (juveniles, young and old adults) at parasite exposure on host susceptibility, fecundity and survival as well as parasite transmission, using two clones of the water flea Daphnia magna and two clones of its bacterial parasite Pasteuria ramosa.

Younger D. magna were more susceptible to infection than older ones, regardless of host or parasite clone. Also, younger‐infected D. magna became castrated faster than older hosts, but host and parasite clone effects contributed to this trait as well. Furthermore, the early‐infected D. magna produced considerably more parasite transmission stages than late‐infected ones, while host age at exposure did not affect virulence as it is defined in models (host mortality).

When virulence is defined more broadly as the negative effects of infection on host fitness, by integrating the parasitic effects on host fecundity and mortality, then host age at exposure seems to slide along a negative relationship between host and parasite fitness. Thus, the virulence–transmission trade‐off differs strongly among age classes, which in turn affects predictions of optimal virulence.

Age‐dependent effects on host susceptibility, virulence and parasite transmission could pose an important challenge for experimental and theoretical studies of infectious disease dynamics and disease ecology. Our results present a call for a more explicit stage‐structured theory for disease, which will incorporate age‐dependent epidemiological parameters.
What Future for the Ombudsman?
Authors: O'Brien Nick 
Published: February 2015

AbstractThe ombudsman institution, in both the public and private sectors, is increasingly identified with the ethos of consumerism and the protection of consumer rights. The current trend is exemplified and reinforced by the EU ADR Directive and by the government response to a recent inquiry into complaints conducted by the Public Administration Select Committee. This article argues that the dominant consumerist ethos diminishes the ability of the ombudsman institution to fulfil its potential. If the ombudsman institution, in particular as manifest in the office of the UK Parliamentary Ombudsman, is to serve the public interest, it must instead promote human rights principles and constitutional morality, adopt a process that is marked by public reasoning and participation and seek by a whole‐system approach to realise a vision that is integrated and truly democratic.
Egg trait variation in a large hawk‐cuckoo (Hierococcyx sparverioides) host population of Chinese babax (Babax lanceolatus)
Authors: YANG Canchao , LIU Yang , LIANG Wei 
Published: February 2015

AbstractMutual interaction between brood parasites and their hosts is a well‐known model system for studying host–parasite coevolution. Both parties have acted reciprocally, resembling an evolutionary arms race, in which adaptations and counter‐adaptations have evolved as a result of host–parasite dynamics, such as the classical cuckoo–host system. Discrimination among parasite and cuckoo eggs and rejection of foreign eggs is regarded as an important anti‐parasitism strategy. The Chinese babax (Babax lanceolatus) is a large hawk‐cuckoo (Hierococcyx sparverioides) host distributed in southwest China. A previous study shows that the babax is an intermediate egg rejector, and most cuckoo eggs are accepted by the Chinese babax, although a small proportion of hosts reject cuckoo eggs. Interestingly, the large hawk‐cuckoo lays non‐mimetic eggs in contrast to the uniform blue eggs of babaxes. Because egg coloration is a critical cue used by host species in favor of the recognition of parasitic eggs by hosts, we used a spectrometer to quantify egg color variation to understand the differentiation in discrimination ability between the egg rejectors and acceptors. We found that the chroma of intra‐clutch variation of babax eggs was more consistent in egg rejectors than in acceptors. However, no statistical significance was found in inter‐clutch variation between these two types of hosts. Our results suggest that hosts lay eggs with a low level of intra‐clutch variation without the necessity of a high level of inter‐clutch variation simultaneously as predicted by the egg signature hypothesis. This study may further indicate that selection pressures from evolutionarily recent parasites can drive individual‐based differences in an anti‐parasitism strategy.
One hundred years of population ecology: Successes, failures and the road ahead
Authors: KREBS Charles J. 
Published: February 2015

AbstractPopulation ecology is the most mature of the three subdisciplines of ecology partly because it has a solid mathematical foundation and partly because it can address the primary questions of distribution and abundance with experimental protocols. Yet there is much left to do to integrate our population knowledge into community and ecosystem ecology to help address the global issues of food security and the conservation of biodiversity. Many different approaches are now being developed to bring about this integration and much more research will be necessary to decide which if any will be most useful in achieving our goals of explaining the changes we see in the distribution and abundance of animals and plants. Food web ecology would appear to be the best approach at present because it uses the detailed information of the population ecology of particular species in combination with data on consumer–resource interactions to apply to the applied problems of biodiversity conservation, food security, pest management and disease prevention. If we can use our understanding of population ecology to address the practical problems of our time in a creative way, we will benefit both the human population and the Earth's biodiversity. Much remains to be done.