bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental duration and predator satiation levels systematically affect functional response parameters
Authors: Li Yuanheng , Rall Björn C. , Kalinkat Gregor 
Published: March 2017

AbstractEmpirical feeding studies where density-dependent consumption rates are fitted to functional response models are often used to parametrize the interaction strengths in models of population or food-web dynamics. However, the relationship between functional response parameter estimates from short-term feeding studies and real-world, long-term, trophic interaction strengths remains largely untested. In a critical first step to address this void, we tested for systematic effects of experimental duration and predator satiation on the estimation of functional response parameters, namely attack rate and handling time. Analyzing a large data set covering a wide range of predator taxonomies and body sizes we show that attack rates decrease with increasing experimental duration, and that handling times of starved predators are consistently shorter than those of satiated predators. Therefore, both the experimental duration and the predator satiation level have a strong and systematic impact on the predictions of population dynamics and food-web stability. Our study highlights potential pitfalls at the intersection of empirical and theoretical applications of functional responses. We conclude our study with some practical suggestions how these implications should be addressed in the future to improve predictive abilities and realism in models of predator-prey interactions.
High variability impairs motor learning regardless of whether it affects task performance
Authors: Cardis Marco , Casadio Maura , Ranganathan Rajiv 
Published: March 2017

AbstractMotor variability plays an important role in motor learning, although the exact mechanisms of how variability affects learning is not well understood. Recent evidence suggests that motor variability may have different effects on learning in redundant tasks, depending on whether it is present in the task space (where it affects task performance), or in the null space (where it has no effect on task performance). Here we examined the effect of directly introducing null and task space variability using a manipulandum during the learning of a motor task. Participants learned a bimanual shuffleboard task for 2 days, where their goal was to slide a virtual puck as close as possible towards a target. Critically, the distance traveled by the puck was determined by the sum of the left and right hand velocities, which meant that there was redundancy in the task. Participants were divided into five groups – based on both the dimension in which the variability was introduced and the amount of variability that was introduced during training. Results showed that although all groups were able to reduce error with practice, learning was affected more by the amount of variability introduced rather than the dimension in which variability was introduced. Specifically, groups with higher movement variability during practice showed larger errors at the end of practice compared to groups that had low variability during learning. These results suggest that although introducing variability can increase exploration of new solutions, this may come at a cost of decreased stability of the learned solution.
Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test
Authors: Toro Israel Del , Berberich Gabriele , Ribbons Relena R. , Berberich Martin B. , Sanders Nathan J. , Ellison Aaron M. 
Published: March 2017

AbstractEcological studies aim to better understand the distribution and abundances of organisms. Yet ecological works often are subjected to unintentional biases thus an improved framework for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants(Formica rufa,RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 meters of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE-SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.
Evolution of the sex ratio and effective number under gynodioecy and androdioecy
Authors: Uyenoyama Marcy K. , Takebayashi Naoki 
Published: March 2017

AbstractWe address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own genotype, while in our maternal control models, it depends on the genotype of its maternal parent. Our analysis unifies full multi-dimensional local stability analysis with the Li-Price equation, which for all its heuristic appeal, describes evolutionary change over a single generation. We define a point in the neighborhood of a fixation state from which a single-generation step indicates the asymptotic behavior of the frequency of a modifier allele initiated at an arbitrary point near the fixation state. A concept of heritability appropriate for the evolutionary modification of sex emerges from the Li-Price framework. We incorporate our theoretical analysis into our previously-developed Bayesian inference framework to develop a new method for inferring the viability of gonochores (males or females) relative to hermaphrodites. Applying this approach to microsatellite data derived from natural populations of the gynodioecious plantSchiedea salicariaand the androdioecious killifishKryptolebias marmoratus, we find that while female and hermaphroditeS. salicariaappear to have similar viabilities, maleK. marmoratusappear to survive to reproductive age at less than half the rate of hermaphrodites.
Novelty by Furcation and Fusion: How tree-like is evolution?
Authors: Oakley Todd H. 
Published: March 2017

AbstractNovelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study novelty phylogenetically, with a key question of whether evolution occurs by tree-like branching, or through exchange of distantly related parts in processes akin to horizontal transfer. Here, I argue that except at the lowest levels of biological organization, evolution is not usually tree-like. Perfectly vertical inheritance, an assumption of evolutionary trees, requires simultaneous co-duplication of all the parts of a duplicating or speciating (which I collectively call 'furcating') biological feature. However, simultaneous co-duplication of many parts usually requires variational processes that are rare. Therefore, instead of being perfectly tree-like, evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression and co-option are such fusion processes at different levels of organization. In addition to co-duplication, units under phylogenetic study must individuate (gaining evolutionary independence) before they can diverge. A lack of individuation erases evolutionary history, and provides another challenge to tree-like evolution. In particular, biological units in the same organism that are the products of development always share the same genome, perhaps making full individuation difficult. The ubiquity of processes that fuse distantly related parts or oppose individuation has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be violated, to the point where we may need a different metaphor, such as economic public goods, or a ‘web of life’. Secondly, we may need to expand current models. For example, even under the prevailing model of cell-type evolution, the sister-cell-type model, a lack of complete individuation and evolution by co-option will often be involved in forming new cell-types. Finally, these processes highlight a need for an expansive toolkit for studying evolutionary history. Multivariate methods are particularly critical to discover co-variation, the hallmark of an absence of complete individuation. In addition to studying phylogenetic trees, we may often need to analyze and visualize phylogenetic networks. Even though furcation - the splitting and individuation of biological features - does happen, fusion of distant events is just as critical for the evolution of novelties, and must formally be incorporated into the metaphors, models, and visualization of evolutionary history.
Salt-bridge Networks within Globular and Disordered Proteins – Characterizing Trends for Designable Interactions
Authors: Basu Sankar , Mukharjee Debasish 
Published: March 2017

AbstractThere has been fare amount of debate regarding the contribution of salt-bridges in the stabilization of protein folds. However, their participation in crucial protein functions are well established. The current study analyzes their modes of association, in terms of networks, both within globular proteins and also at protein-protein interfaces. Apart from the most common and trivial case of isolated salt-bridges, bifurcated salt-bridges appear to be a special salt-bridge motif both in terms of its topology and geometry and found ubiquitously in proteins and inter-protein complexes. Interesting and attractive examples presenting different interaction-modes have been highlighted. Bifurcated salt-bridges appear to function as molecular clips instrumental in stitching large surface contours of interacting protein-protein interfaces. The work also emphasizes the key role of salt-bridge mediated interactions in the partial folding of proteins containing large amount of disordered regions. Salt-bridge mediated interactions seem pivotal in promoting ‘disorder-to-order’ transitions for small disordered protein fragments and their stabilization upon binding. The results should guide to elucidate the modus operandi of these partially disordered proteins and also should be helpful to conceptualize how these proteins manage to keep necessary amount of disorder even in their functionally active bound forms, encouraging future studies. It should also be potentially beneficial towards the proposed notion of geometrically specific designable interactions involving salt-bridges.
Assessing the relationship of ancient and modern populations
Authors: Schraiber Joshua G. 
Published: March 2017

AbstractGenetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error and post-mortem damage by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequence more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high cover-age individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.
Coral reefs in crisis: The reliability of deep-time food web reconstructions as analogs for the present
Authors: Roopnarine Peter D. , Dineen Ashley A. 
Published: March 2017

AbstractOngoing anthropogenic alterations of the biosphere have shifted emphasis in conservation biology from individual species to entire ecosystems. Modern measures of ecosystem change, however, lack the extended temporal scales necessary to forecast future change under increasingly stressful environmental conditions. Accordingly, the assessment and reconstruction of ecosystem dynamics during previous intervals of environmental stress and climate change in deep time has garnered increasing attention. The nature of the fossil record, though, raises questions about the difficulty of reconstructing paleocommunity and paleoecosystem-level dynamics. In this study, we assess the reliability of such reconstructions by simulating the fossilization of a highly threatened and disturbed modern ecosystem, a Caribbean coral reef. Using a high-resolution coral reef food web from Jamaica, we compare system structures of the modern and simulated fossil reefs, including guild richness and evenness, trophic level distribution, predator dietary breadth, food chain lengths, and modularity. Results indicate that despite the loss of species, guilds, and trophospecies interactions, particularly zooplankton and other soft-bodied organisms, the overall guild diversity, structure, and modularity of the reef ecosystem remained intact. These results have important implications for the integrity of fossil food web studies and coral reef conservation, demonstrating that fossil reef communities can be used to understand reef community dynamics during past regimes of environmental change.
Abnormally high levels of serum α-klotho result in a poor outcome for clinical pregnancy-A prospective cohort study
Authors: Funabiki Miyako , Taguchi Sagiri , Nakamura Yoshitaka 
Published: March 2017

AbstractBackgroundThe klotho protein has been extensively studied. However, there are no studies examining the association between serum alpha klotho levels and the clinical outcome of post-clinical pregnancy.MethodsWe conducted a prospective cohort study in 42 patients (median age 37.4 years) to evaluate the association between serum alpha klotho levels during the follicular phase of preimplantation and the clinical outcome data of post-clinical pregnancy. The patients provided informed consent at our clinic. The serum alpha klotho levels were evaluated using a human soluble alpha klotho assay kit. The fetal chromosomal abnormalities were investigated at our clinic. We also assessed the clinical outcomes of post-clinical pregnancies.ResultsThe serum alpha klotho level during the follicular phase of preimplantation for non-pregnant women was 544.31 pg/ml (mean). The clinical pregnancy rate was 38.1%. There were chromosomal abnormalities observed in four unborn children (9.5%; Down syndrome, etc). The serum alpha klotho levels during the follicular phase of preimplantation in the chromosomal abnormalities group were higher than in the group without chromosomal abnormalities (P=0.029, abnormalities group 659.26 pg/ml [mean] versus control 530.23 pg/ml [mean]). A multiple logistic regression analysis showed the chromosomal abnormalities rates in unborn children were positively influenced by serum alpha klotho levels during the follicular phase of preimplantation (p=0.0008) and the patient’s age (p=0.008).ConclusionPrevious studies have demonstrated that increased alpha klotho levels in human serum are positively correlated with health. However, abnormally high levels of serum alpha klotho during the follicular phase of preimplantation may predict a poor outcome for clinical pregnancy.
Combining molecular gut content analysis and functional response models shows how body size affects prey choice in soil predators
Authors: Eitzinger Bernhard , Rall Björn C. , Traugott Michael , Scheu Stefan 
Published: March 2017

SummaryPredator-prey interactions are a core concept of animal ecology and functional response models provide a powerful tool to predict the strength of trophic links and assess motives for prey choice. However, due to their reductionist set-up, these models may not display field conditions, possibly leading to skewed results.We tested the validity of functional response models for multiple prey by comparing them with empirical data from DNA-based molecular gut content analysis of two abundant and widespread macrofauna soil predators, lithobiid and geophilomorph centipedes.We collected soil and litter dwelling centipedes, screened their gut contents for DNA of nine abundant decomposer and intraguild prey using specific primers and tested for different prey and predator traits explaining prey choice. In order to calculate the functional response of same predators, we used natural prey abundances and functional response parameters from published experiments and compared both approaches.Molecular gut content results showed that prey choice of centipedes is driven by predator body size and prey identity. Results of functional response models significantly correlated with results from molecular gut content analysis for the majority of prey species.Overall, the results suggest that functional response models are a powerful tool to predict trophic interactions in soil, however, species-specific traits have to be taken into account to improve predictions.
Bayesian weighing of electron cryo-microscopy data for integrative structural modeling
Authors: Bonomi Massimiliano , Hanot Samuel , Greenberg Charles H. , Sali Andrej , Nilges Michael , Vendruscolo Michele , Pellarin Riccardo 
Published: March 2017

SummaryCryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map and other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-sourceIntegrative Modeling Platform(http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.HighlightsWe present a modeling approach to integrate cryo-EM data with other sources of informationWe benchmark our approach using synthetic data on 21 complexes of known structureWe apply our approach to the GroEL/GroES, RNA polymerase II, and exosome complexes
Substrate-triggered position-switching of TatA and TatB is an essential step in theEscherichia coliTat protein export pathway
Authors: Habersetzer Johann , Moore Kristoffer , Cherry Jon , Buchanan Grant , Stansfeld Phillip , Palmer Tracy 
Published: March 2017

AbstractThe twin arginine protein transport (Tat) machinery mediates the translocation of folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. TheEscherichia coliTat system comprises TatC and two additional sequence-related proteins, TatA and TatB. Here we use disulfide crosslinking and molecular modelling to show there are two binding sites for TatA/B proteins on TatC. TatA and TatB are each able to occupy both sites if they are the only TatA/B protein present. However, under resting conditions the sites are differentially occupied with TatB occupying the ‘polar cluster’ site while TatA binds adjacently at the TatC transmembrane helix 6 binding site. When the Tat system is activated by the overproduction of a substrate, TatA and TatB switch their binding sites. We propose that this substrate-triggered positional exchange is a key step in the assembly of an active Tat translocase.
Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants
Authors: Sanders Jon G , Lukasik Piotr , Frederickson Megan E , Russell Jacob A , Koga Ryuichi , Knight Rob , Pierce Naomi E 
Published: March 2017

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis
Authors: Mungall Christopher J. , Holmes Ian H. 
Published: March 2017

AbstractA common technique for interpreting experimentally-identified lists of genes is to look for enrichment of genes associated to particular ontology terms. The most common technique uses the hypergeometric distribution; more recently, a model-based approach was proposed. These approaches must typically be run using downloaded software, or on a server. We develop a collapsed likelihood for model-based gene set analysis and present WTFgenes, an implementation of both hypergeometric and model-based approaches, that can be published as a static site with computation run in JavaScript on the user's web browser client. Apart from hosting files, zero server resources are required: the site can (for example) be served directly from Amazon S3 or GitHub Pages. A C++11 implementation yielding identical results runs roughly twice as fast as the JavaScript version. WTFgenes is available fromhttps://github.com/evoldoers/wtfgenesunder the BSD3 license. A demonstration for the Gene Ontology is usable athttps://evoldoers.github.io/wtfgo. Contact: Ian Holmesihholmes+wtfgenes@gmail.com.