bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic evidence for population-specific responses to coevolving parasites in a New Zealand freshwater snail
Authors: Bankers Laura , Fields Peter , McElroy Kyle E. , Boore Jeffrey L. , Logsdon John M. , Neiman Maurine 
Published: March 2016

AbstractReciprocal coevolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of coevolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwatersnail Potamopyrgus antipodarumand its coevolving sterilizing trematode parasite,Microphallussp., a textbook example of natural coevolution. We found thatMicrophallus-infectedP. antipodarumexhibit systematic downregulation of genes relative to uninfectedP. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population-level coevolution is leading to population-specific host-parasite interactions and evolutionary trajectories. We also used anFST-based approach to identify a set of loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to coevolving infection in theP. antipodarum-Microphallusinteraction and provide new insights into the genomic basis of coevolutionary interactions in nature.
Glycerol is the actuator of integral feedback control in yeast osmotic stress signaling
Authors: Rutherford Suzannah 
Published: March 2016

AbstractIn a 2009 article in Cell van Oudenaarden and colleagues employed elegant experiments and control theory to model perfect adaptation of the yeast osmotic stress response – precise return of turgor pressure to its optimal, steady-state value despite variation in system parameters and the continued presence of osmotic stress. Their data convincingly showed that nuclear signaling and cell volume undergo “robust perfect adaptation” implying that integral feedback must restore their steady state values. However, the authors incorrectly mapped the integrator onto a minimal network that violates assumptions implicit in conventional block diagrams. Using known features of osmotic stress signaling and results presented by the authors, I argue that glycerol concentration – the integral of the rate of glycerol accumulation (synthesis minus leakage) – transforms metabolic energy into an increased osmolarity that drives water influx and restoration of turgor pressure. I show how integral feedback control actuated through glycerol synthesis is logically positioned to provide perfect adaptation and robustness in hyperosmotic stress responses.
Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria
Authors: Baltrus David A. , Dougherty Kevin , Arendt Kayla R. , Huntemann Marcel , Clum Alicia , Pillay Manoj , Palaniappan Krishnaveni , Varghese Neha , Mikhailova Natalia , Stamatis Dimitrios , Reddy T. B. K. , Ngan Chew Yee , Daum Chris , Shapiro Nicole , Markowitz Victor , Ivanova Natalia , Kyrpides Nikos , Woyke Tanja , Arnold A. Elizabeth 
Published: March 2016

AbstractFungi interact closely with bacteria both on the surfaces of hyphae, and within their living tissues (i.e., endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts, and can mediate a diverse phenotypic traits in their hosts. Although EHB have been observed in many major lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features found across all EHB strains. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, genomes of these facultative EHB resemble those of closely related strains isolated from environmental sources. Although all analyzed genomes encode structures that can be used to interact with eukaryotic hosts, we find no known pathways that facilitate intimate EHB-fungal interactions in all strains. We isolated two strains with nearly identical genomes from different classes of fungi, consistent with previous suggestions of horizontal transfer of EHB across endophytic hosts. Because bacteria are differentially present during the fungal life cycle, these genomes could shed light on the mechanisms of plant growth promotion by fungal endophytes during the symbiotic phase as well as degradation of plant material during saprotrophic and reproductive phases. Given the capacity of EHB to influence fungal phenotypes, these findings illuminate a new dimension of fungal biodiversity.
Experimental evidence for sexual selection against inbred males when it truly counts
Authors: Vega-Trejo Regina , Head Megan L. , Keogh J. Scott , Jennions Michael D. 
Published: March 2016

AbstractAlthough there are many correlational studies, unbiased estimates of inbreeding depression only come from experimental studies that create inbred and outbred individuals. Few such studies determine the extent to which inbreeding depression in males is due to natural or sexual selection. Importantly, traits that are closely related to fitness are predicted to be most strongly affected by inbreeding depression, so measuring fitness or key fitness components, rather than phenotypic traits, is necessary to estimate inbreeding depression accurately. Here, we experimentally created inbred and outbred male mosquitofish (Gambusia holbrooki) by mating full-sibs (f=0.25). We show this led to a 23% reduction in genome-wide heterozygosity. Males were then raised on different diets early in life. We then allowed adult males to compete freely for females to test if inbreeding, early diet, and their interaction affect a male’s share of paternity. Early diet had no effect on paternity, but outbred males sired almost twice as many offspring as inbred males. We also found that males with a relatively long gonopodium (intromittent organ) had greater reproductive success. We demonstrate that inbreeding has important consequences because it negatively affects a key component of male fitness. Given there was no difference in adult mortality this finding can only be due to inbreeding negatively affecting sexually selected traits.
Sexual selection on body size, genitals and heterozygosity:effects of demography and habitat complexity
Authors: Head Megan L. , Kahn Andrew T. , Keogh J. Scott , Jennions Michael D. 
Published: March 2016

AbstractEnvironmental variation can maintain genetic variation in sexually selected traits if it affects the strength of directional selection. Specifically, environmental variation in sex-specific mortality will change the operational sex ratio (OSR), which predicts the intensity of mating competition. How the OSR affects selection for specific male traits is poorly understood; and it is unknown how often sexual selection is affected by interactions between the OSR and environmental factors that alter social variables such as mate encounter rates. Here, we experimentally manipulated the OSR and habitat complexity and quantified sexual selection on male mosquitofish (Gambusia holbrooki). InG. holbrookithere is high within-population variation in male size, which may exist because of a tradeoff between the ability to sneak copulate (favouring small males) and monopolize females (favouring large males). The success of each tactic is predicted to depend on the OSR, encounter rates and the ability to stealthily approach conspecifics. We show that, despite greater sharing of paternity under a male-biased OSR, neither the opportunity for selection, nor selection on male traits was affected by the OSR or habitat complexity. Instead, sexual selection consistently favored smaller males with high genetic heterozygosity (using >3000 SNP markers), and a relatively long gonopodium (intromittent organ).
Are sexually selected traits affected by a poor environment early in life?
Authors: Vega-Trejo Regina , Jennions Michael D. , Head Megan L. 
Published: March 2016

AbstractConditions experienced early in life can affect key life-history traits. Individuals that experience a poor nutritional environment early in life can reduce potential costs by delaying sexual maturation. The direct costs of delaying maturation are well known (i.e. delayed onset of breeding), but individuals can also face additional costs as adults. Some of these ‘hidden costs’ accrue due to cryptic morphological and physiological changes. In mosquitofish (Gambusia holbrooki), males with limited food intake early in life delay maturation to eventually reach a similar adult body size to their well-fed counterparts (‘catch-up growth’). Here we tested whether a poor diet early in life incurs hidden costs due to reduced expression of sexually selected male traits (genital size and ejaculate traits). We found that diet early in life significantly influenced sperm reserves and replenishment rate due to age and development-rate dependent effects. Although catching-up in body size ameliorates some of the costs of a poor start in life for males, our findings suggest that long-term fitness costs might arise because of sexually selection against these males. Our results highlight that fitness costs of a poor start in life can extend into adulthood.
GDP to GTP exchange on the microtubule end can contribute to the frequency of catastrophe
Authors: Piedra Felipe-Andrés , Kim Tae , Garza Emily S. , Geyer Elisabeth A. , Burns Alexander , Ye Xuecheng , Rice Luke M. 
Published: March 2016

ABSTRACTMicrotubules are dynamic polymers of αβ-tubulin that have essential roles in chromosome segregation and organizing the cytoplasm. Catastrophe – the switch from growing to shrinking – occurs when a microtubule loses its stabilizing GTP cap. Recent evidence indicates that the nucleotide on the microtubule end controls how tightly an incoming subunit will be bound (trans-acting GTP), but most current models do not incorporate this information. We implemented transacting GTP into a computational model for microtubule dynamics. In simulations, growing microtubules often exposed terminal GDP-bound subunits without undergoing catastrophe. Transient GDP exposure on the growing plus end slowed elongation by reducing the number of favorable binding sites on the microtubule end. Slower elongation led to erosion of the GTP cap and an increase in the frequency of catastrophe. Allowing GDP to GTP exchange on terminal subunits in simulations mitigated these effects. Using mutant αβ-tubulin or modified GTP, we showed experimentally that a more readily exchangeable nucleotide led to less frequent catastrophe. Current models for microtubule dynamics do not account for GDP to GTP exchange on the growing microtubule end, so our findings provide a new way of thinking about the molecular events that initiate catastrophe.
Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets
Authors: Narechania Apurva , Baker Richard , DeSalle Rob , Mathema Barun , Kolokotronis Sergios-Orestis , Kreiswirth Barry , Planet Paul J. 
Published: March 2016

AbstractBackgroundCollective animal behavior such as the flocking of birds or the shoaling of fish has inspired a class of algorithms designed to optimize distance-based clusters in various applications including document analysis and DNA microarrays. In the flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize and clusters emerge without the need for partitional seeds. In addition to their unsupervised nature, flocking offers several computational advantages including the potential to decrease the number of required comparisons.FindingsIn Clusterflock, we implement a flocking algorithm designed to find groups (flocks) of orthologous gene families (OGFs) that share a common evolutionary history. Pairwise distances that measure the phylogenetic incongruence between OGFs guide flock formation. We test this approach on several simulated datasets varying the number of underlying topologies, the proportion of missing data, and evolutionary rates, and show that in datasets containing high levels of missing data and rate heterogeneity, clusterflock outperforms other well-established clustering techniques. We also demonstrate its utility on a known, large-scale recombination event inStaphylococcus aureus. By isolating sets of OGFs with divergent phylogenetic signal, we can pinpoint the recombined region without forcing a pre-determined number of groupings or defining a pre-determined incongruence threshold.ConclusionsClusterflock is an open source tool that can be used to discover horizontally transferred genes, recombining areas of chromosomes, and the phylogenetic “core” of a genome. Though we use it in an evolutionary context, it is generalizable to any clustering problem. Users can write extensions to calculate any distance metric on the unit interval and use these distances to flock any type of data.
Distinct Responses to Reduplicated Chromosomes Require Distinct Mad2 Responses
Authors: Stormo Benjamin M. , Fox Donald T. 
Published: March 2016

ABSTRACTDuplicating chromosomes once each cell cycle produces sister chromatid pairs, which separate accurately at anaphase. In contrast, reduplicating chromosomes without separation frequently produces polytene chromosomes, a barrier to accurate mitosis. Chromosome reduplication occurs in many contexts, including: polytene tissue development, polytene tumors, and following treatment with mitosis-blocking chemotherapeutics. However, mechanisms responding to or resolving polyteny during mitosis are poorly understood. Here, usingDrosophila, we uncover two distinct reduplicated chromosome responses. First, when reduplicated polytene chromosomes persist into metaphase, an anaphase delay prevents tissue malformation and apoptosis. Second, reduplicated polytene chromosomes can also separate prior to metaphase through a spindlePindependent mechanism termed Separation-Into-Recent-Sisters (SIRS). Both reduplication responses require the spindle assembly checkpoint protein Mad2. While Mad2 delays anaphase separation of metaphase polytene chromosomes, Mad2’s control of overall mitotic timing ensures efficient SIRS. Our results pinpoint mechanisms enabling continued proliferation after genome reduplication, a finding with implications for cancer progression and prevention.
Case-control association mapping without cases
Authors: Liu Jimmy Z , Erlich Yaniv , Pickrell Joseph K 
Published: March 2016

AbstractThe case-control association study is a powerful method for identifying genetic variants that influence disease risk. However, the collection of cases can be time-consuming and expensive; if a disease occurs late in life or is rapidly lethal, it may be more practical to identify family members of cases. Here, we show that replacing cases with their first-degree relatives enables genome-wide association studies by proxy (GWAX). In randomly-ascertained cohorts, this approach enables previously infeasible studies of diseases that are absent (or nearly absent) in the cohort. As an illustration, we performed GWAX of 12 common diseases in 116,196 individuals from the UK Biobank. By combining these results with published GWAS summary statistics in a meta-analysis, we replicated established risk loci and identified 17 newly associated risk loci: four in Alzheimer’s disease, eight in coronary artery disease, and five in type 2 diabetes. In addition to informing disease biology, our results demonstrate the utility of association mapping using family history of disease as a phenotype to be mapped. We anticipate that this approach will prove useful in future genetic studies of complex traits in large population cohorts.
Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids
Authors: Santiago James P. , Tegeder Mechthild 
Published: March 2016

Abstract
Allocation of large amounts of nitrogen to developing organs occurs in the phloem and is essential for plant growth and seed development. In Arabidopsis (Arabidopsis thaliana) and many other plant species, amino acids represent the dominant nitrogen transport forms in the phloem, and they are mainly synthesized in photosynthetically active source leaves. Following their synthesis, a broad spectrum of the amino nitrogen is actively loaded into the phloem of leaf minor veins and transported within the phloem sap to sinks such as developing leaves, fruits, or seeds. Controlled regulation of the source-to-sink transport of amino acids has long been postulated; however, the molecular mechanism of amino acid phloem loading was still unknown. In this study, Arabidopsis AMINO ACID PERMEASE8 (AAP8) was shown to be expressed in the source leaf phloem and localized to the plasma membrane, suggesting its function in phloem loading. This was further supported by transport studies with aap8 mutants fed with radiolabeled amino acids and by leaf exudate analyses. In addition, biochemical and molecular analyses revealed alterations in leaf nitrogen pools and metabolism dependent on the developmental stage of the mutants. Decreased amino acid phloem loading and partitioning to sinks led to decreased silique and seed numbers, but seed protein levels were unchanged, demonstrating the importance of AAP8 function for sink development rather than seed quality. Overall, these results show that AAP8 plays an important role in source-to-sink partitioning of nitrogen and that its function affects source leaf physiology and seed yield.
Liberal Interventionism
Authors: Lipsey David 
Published: March 2016

AbstractDavid Lipsey analyses the arguments made by former Labour prime minister Tony Blair in his Chicago speeches for armed liberal intervention in states which are abusing the human rights of their citizens. He traces these arguments back to previous advocates of such intervention such as W. E. Gladstone and Woodrow Wilson. The arguments of Blair and advocates are often compelling in principle. However, in most cases—Iraq and Libya are examples—the practical consequences of military action turn out to be disastrous. Though opposing pacifism, and the ill‐thought‐out hostility to all things military of Labour's current leader Jeremy Corbyn, Lipsey's advice to those thinking of intervening is: don't.
Planning Makes (Closer to) Perfect: Exploring United States’ Local Government Officials’ Evaluations of Crisis Management
Authors: Avery Elizabeth Johnson , Graham Melissa , Park Sejin 
Published: March 2016

How a government responds to, manages, and communicates about crisis has direct implications for public well‐being and ultimately shapes public opinion about local governments and government officials. Yet, little is known about crisis preparation, especially that of local governments. Local governments are involved in managing any crisis situation that affects their communities, regardless of the responsible organization or nature of the crisis. This study surveys local government officials (N = 307) in 44 states across the United States who manage crisis communication to reveal unique considerations of planning, magnitude and citizen satisfaction on crisis management. Novel findings are revealed with respect to each variable to direct future crisis research, particularly that informing the precrisis stage.
A Bayesian approach for detecting the impact of mass‐extinction events on molecular phylogenies when rates of lineage diversification may vary
Authors: May Michael R. , Höhna Sebastian , Moore Brian R. 
Published: March 2016

SummaryThe paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass‐extinction events on molecular phylogenies, even in the presence of tree‐wide diversification‐rate variation and in the absence of additional information from the fossil record.Our approach is based on an episodic stochastic‐branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree‐wide shifts in speciation rate; (ii) instantaneous tree‐wide shifts in extinction rate and (iii) instantaneous tree‐wide mass‐extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event‐specific rate parameters. The magnitude of each event is drawn from an event‐specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible‐jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree‐wide diversification‐rate variation and mass‐extinction events by specifying a biologically informed prior on the magnitude of mass‐extinction events and empirical hyperpriors on the diversification‐rate parameters.We demonstrate via simulation that this method has substantial power to detect the number of mass‐extinction events and provides unbiased estimates of the timing of mass‐extinction events, while exhibiting an appropriate (i.e. <5%) false‐discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma.This new approach – the CPP on Mass‐Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass‐extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Dentists' restorative decision‐making and implications for an ‘amalgamless’ profession. Part 3: Dentists' attitudes
Authors: Alexander G , Hopcraft MS , Tyas MJ , Wong RHK 
Published: March 2016

AbstractBackgroundThe Minamata Convention has agreed to a worldwide reduction in the production and use of mercury‐containing products and processes. This will change the approach to use of direct restorative materials in the future. There is little research exploring the attitudes of dentists to any change.MethodsA survey relating to the use of direct restorative materials was distributed to dentists who were members of the Australian Dental Association or Members and Fellows of the Royal Australasian College of Dental Surgeons. Data were statistically analysed.ResultsThere were 408 respondents. Responses to statements concerning attitudes toward a phase‐down of amalgam depended on whether the respondent used amalgam, year of primary dental qualification and association with academia. Thirty per cent of respondents indicated they do not use amalgam. The mean use of amalgam for all direct restorative procedures was 18%.ConclusionsDentists are concerned over potential implications of a phase‐down of amalgam and much should be done to address these concerns. Many dentists are undecided as to what are the implications, which may reflect a lack of understanding of the issues. It is incumbent on policy‐makers to produce and disseminate information relating to the issues identified by this research.