bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Coevolutionary Romance of Social Learning and Parasitic Behavior
Authors: McElreath Richard 
Published: May 2016

AbstractOnce an animal begins to acquire behavior by social learning, it may be seduced by parasitic parasitic, behavior that reduces the animal’s fitness and thereby increases its own spread. However, the animal’s psychology will coevolve, potentially limiting the influence and spread of parasitic behavior. I revisit prominent models of the evolution of social learning and introduce the possibility of parasitic behavior. First, I explore a courtship between primitive social learning and parasitic behavior. Parasitic behavior can spread, but selection on the host then reduces social learning and limits its importance. Both parties are frustrated. In the second part, I study a reconciliation dynamic in which social learning becomes strategic about who it partners with. In this model, parasitic behavior can become prevalent and substantially reduce host fitness. However, it may also evolve to be mutualistic and raise the mean fitness of the host organism. When this occurs, natural selection may favor psychological susceptibility to parasitic behavior. Both social learning and socially learned behavior can enjoy a happy ending.
Improved Insights into Protein Thermal Stability: From the Molecular to the Structurome Scale
Authors: Pucci Fabrizio , Rooman Marianne 
Published: May 2016

AbstractDespite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multi-scale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analyzed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability - at the structurome level - contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of thermostable and mesostable proteins differ. Some final considerations on how the multi-scale approach could help unraveling the protein stability mechanisms are briefly discussed.
Scale-free versus multi-scale: Statistical analysis of livestock mobility patterns across species
Authors: Sakamoto Takuto , Sanders Lloyd , Inazumi Nobu 
Published: May 2016

ABSTRACTIn quantitative studies on animal movements and foraging, there has been ongoing debate over the relevance of Lévy walk and related stochastic models to understanding mobility patterns of diverse organisms. In this study, we collected and analyzed a large number of GPS logs that tracked the movements of different livestock species in northwestern Kenya. Statistically principled analysis has only found limited evidence for the scale-free movement patterns of the Lévy walk and its variants, even though most of the tracked movements clearly show super-diffusive behavior within the relevant temporal duration. Instead, the analysis has given strong support to composite exponential distributions (composite Brownian walks) as the best description of livestock movement trajectories in a wide array of parameter settings. Furthermore, this support has become overwhelming and near universal under an alternative criterion for model selection. These results illuminate the multi-scale and multi-modal nature of livestock spatial behavior. They also have broader theoretical and empirical implications for the related literature.
Tribe: The collaborative platform for reproducible web-based analysis of gene sets
Authors: Zelaya René A. , Wong Aaron K. , Frase Alex T. , Ritchie Marylyn D. , Greene Casey S. 
Published: May 2016

AbstractBackgroundThe adoption of new bioinformatics webservers provides biological researchers with new analytical opportunities but also raises workflow challenges. These challenges include sharing collections of genes with collaborators, translating gene identifiers to the most appropriate nomenclature for each server, tracking these collections across multiple analysis tools and webservers, and maintaining effective records of the genes used in each analysis.DescriptionIn this paper, we present the Tribe webserver (available athttps://tribe.greenelab.com), which addresses these challenges in order to make multi-server workflows seamless and reproducible. This allows users to create analysis pipelines that use their own sets of genes in combinations of specialized data mining webservers and tools while seamlessly maintaining gene set version control. Tribe’s web interface facilitates collaborative editing: users can share with collaborators, who can then view, download, and edit these collections. Tribe’s fully-featured API allows users to interact with Tribe programmatically if desired. Tribe implements the OAuth 2.0 standard as well as gene identifier mapping, which facilitates its integration into existing servers. Access to Tribe’s resources is facilitated by an easy-to-install Python application calledtribe-client. We provide Tribe and tribe-client under a permissive open-source license to encourage others to download the source code and set up a local instance or to extend its capabilities.ConclusionsThe Tribe webserver addresses challenges that have made reproducible multi-webserver workflows difficult to implement until now. It is open source, has a user-friendly web interface, and provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools.
Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation
Authors: Duarte Fabiana M. , Fuda Nicholas J. , Mahat Dig B. , Core Leighton J. , Guertin Michael J. , Lis John T. 
Published: May 2016

AbstractThe coordinated regulation of gene expression at the transcriptional level is fundamental to organismal development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use Precision Run-On sequencing (PRO-seq) to examine the genome-wide Heat Shock (HS) response inDrosophilaand the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS. We identify the primary HS response genes and the rate-limiting steps in the transcription cycle that GAGA-Associated Factor (GAF) and HS Factor (HSF) regulate. We demonstrate that GAF acts upstream of promoter-proximally paused RNA Polymerase II (Pol II) formation, likely at the step of chromatin opening, and that GAF-facilitated Pol II pausing is critical for HS activation. In contrast, HSF is dispensable for establishing or maintaining Pol II pausing, but is critical for the release of paused Pol II into the gene body at a subset of highly-activated genes. Additionally, HSF has no detectable role in the rapid HS-repression of thousands of genes.
The reciprocal relationship between competition and intraspecific trait variation
Authors: Bennett Jonathan A. , Riibak Kersti , Tamme Riin , Lewis Rob J. , Pärtel Meelis 
Published: May 2016

Summary

Trait differences among plants are expected to influence the outcome of competition; competition should be strongest between similar species (or individuals) under limiting similarity, and between dissimilar species within competitive hierarchies. These hypotheses are often used to infer competitive dynamics from trait patterns within communities. However, plant traits are frequently plastic in response to competition. This variation is poorly accounted for in trait‐based studies of competition and community assembly.

To explore the relationship between trait responses and competitive outcomes, we grew 15 species alone, in monoculture and in mixture. We measured traits relating to leaf and root tissue morphology as well as biomass allocation and related competition‐induced changes in these traits to intra‐ and interspecific competition using multi‐model inference. Additionally, we tested how traits from different competitive environments influenced potential community assembly inferences.

The competitive environment had large effects on species’ traits, although many effects were species specific. Differences among species in how competition affected trait expression were linked to both intra‐ and interspecific competition, frequently affecting competitive hierarchies. Intraspecific competition was lower for species that limited competition‐induced increases in root allocation and had less variability in this trait overall. Interspecific competition was lower for species with larger leaves and lower specific leaf area than their neighbours. Switching to more stress‐tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity affecting competitive outcomes. Moreover, changes in these traits were linked to changes in functional diversity, suggesting that competition affects functional diversity by affecting trait expression.

Synthesis. Both trait hierarchies and trait dissimilarity affect the outcome of competition by acting on different traits, although competition‐induced changes in trait expression can alter competitive outcomes. Moreover, the magnitude of these trait changes suggests that the source environment where plant traits are collected can affect the inferences drawn from trait patterns within communities. Combined, our results suggest that considering the effect of competition on trait expression is critical to understanding the relationship between traits and community assembly.
Soil abiotic and biotic controls on plant performance during primary succession in a glacial landscape
Authors: Castle Sarah C. , Lekberg Ylva , Affleck David , Cleveland Cory C. 
Published: May 2016

Summary

Plant–soil interactions are temporally dynamic in ways that are important for the development of plant communities. Yet, during primary succession, the degree to which changing soil characteristics (e.g. increasing nutrient availabilities) and developing communities of soil biota influence plant growth and species turnover is not well understood.

We conducted a two‐phase glasshouse experiment with two native plant species and soils collected from three ages (early, mid‐ and late succession) of an actively developing glacial chronosequence ranging from approximately 5 to <100 years in age. The first phase assessed how soil abiotic characteristics and soil biota immediately influenced plant performance. In the second phase, we used conditioned soils to grow the same plant species and assessed how the direction and strength of plant–soil feedback (PSF) varied through succession. We used high and low nutrient and soil sterilization treatments to isolate effects of abiotic and biotic factors on plant performance and to assess how patterns of PSF related to soil nutrients.

For both species, our experiments revealed that the initial effect of soil biota on plant performance depended on successional stage. In soils collected from early‐, mid‐ and late‐succession stages, we observed neutral to negative, negative and positive effects of soil biota on plant performance, respectively.

Plant–soil feedback varied with successional stage and depended on whether microcosms were supplied with nutrients. Under low nutrient conditions, soil conditioning by plants, unrelated to initial soil biota, was an important mechanism for positive PSF. Under high nutrient conditions, PSFs differed by plant species in early‐ and mid‐succession soils, but were consistently neutral in late succession.

Synthesis. Soil biota can affect the performance of pioneer plants over short gradients of ecosystem development, but the strength and direction of interactions depend on nutrient availability. Conceptual frameworks describing mechanisms of primary succession should acknowledge soil conditioning by previous plants as a potential mechanism of positive feedback.
A multiproxy approach to evaluate biocidal treatments on biodeteriorated majolica glazed tiles
Authors: Coutinho M. L. , Miller A. Z. , Martin‐Sanchez P. M. , Mirão J. , Gomez‐Bolea A. , Machado‐Moreira B. , Cerqueira‐Alves L. , Jurado V. , Saiz‐Jimenez C. , Lima A. , Phillips A. J. L. , Pina F. , Macedo M. F. 
Published: May 2016

SummaryThe Fishing House located on the grounds of the Marquis of Pombal Palace, Oeiras, Portugal, was built in the 18th century. During this epoch, Portuguese gardens, such as the one surrounding the Fishing House, were commonly ornamented with glazed wall tile claddings. Currently, some of these outdoor tile panels are covered with dark colored biofilms, contributing to undesirable aesthetic changes and eventually inducing chemical and physical damage to the tile surfaces. Phylogenetic analyses revealed that the investigated biofilms are mainly composed of green algae, cyanobacteria and dematiaceous fungi. With the aim of mitigating biodeterioration, four different biocides (TiO2 nanoparticles, Biotin® T, Preventol® RI 80 and Albilex Biostat®) were applied in situ to the glazed wall tiles. Their efficacy was monitored by visual examination, epifluorescence microscopy and DNA‐based analysis. Significant changes in the microbial community composition were observed 4 months after treatment with Preventol® RI 80 and Biotin® T. Although the original community was inactivated after these treatments, an early stage of re‐colonization was detected 6 months after the biocide application. TiO2 nanoparticles showed promising results due to their self‐cleaning effect, causing the detachment of the biofilm from the tile surface, which remained clean 6 and even 24 months after biocide application. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd
Native plasmids restrict growth of Phaeobacter inhibens DSM 17395: Energetic costs of plasmids assessed by quantitative physiological analyses
Authors: Trautwein Kathleen , Will Sabine Eva , Hulsch Reiner , Maschmann Uwe , Wiegmann Katharina , Hensler Michael , Michael Victoria , Ruppersberg Hanna , Wünsch Daniel , Feenders Christoph , Neumann‐Schaal Meina , Kaltenhäuser Sabine , Ulbrich Marcus , Schmidt‐Hohagen Kerstin , Blasius Bernd , Petersen Jörn , Schomburg Dietmar , Rabus Ralf 
Published: May 2016

SummaryPlasmid carriage is associated with energetic costs, and thus only those plasmids providing fitness benefits are stably maintained in the host lineage. Marine bacteria of the Roseobacter clade harbor up to 11 extrachromosomal replicons, adding lifestyle‐relevant and possibly habitat success‐promoting functions to their genomic repertoire. Phaeobacter inhibens DSM 17395 is a nutritionally versatile representative, carrying three stable and functionally distinct plasmids (65, 78, and 262 kb). The present study investigates the physiological and energetic consequences of plasmid carriage in P. inhibens DSM 17395, employing mutants cured from all native plasmids in every possible combination (seven different). Cultivation in process‐controlled bioreactors with casamino acids as organic substrate revealed a complex physiological response, suggesting existence of functional interconnections between the replicons. Deletion of the 262 kb plasmid boosted growth rate (>3‐fold) and growth efficiency (yields for carbon, O2 and CO2), which was not observed for the 65 or 78 kb plasmid. Carriage of the 262 kb plasmid was most costly for the wild type, i.e. contributing ∼50% to its energetic (dissimilatory) expenditures. Cost–benefit analysis of plasmid carriage reflects the high value of plasmids for niche specialization of P. inhibens DSM 17395 and most likely also for related Phaeobacter species.
Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching
Authors: Cardini Ulisse , van Hoytema Nanne , Bednarz Vanessa N. , Rix Laura , Foster Rachel A. , Al‐Rshaidat Mamoon M. D. , Wild Christian 
Published: May 2016

SummaryCoral holobionts (i.e., coral‐algal‐prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral‐associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.
A transposon present in specific strains of Bacillus subtilis negatively affects nutrient‐ and dodecylamine‐induced spore germination
Authors: Krawczyk Antonina O. , Berendsen Erwin M. , de Jong Anne , Boekhorst Jos , Wells‐Bennik Marjon H. J. , Kuipers Oscar P. , Eijlander Robyn T. 
Published: May 2016

SummarySpore germination shows a large inter‐strain variability. Spores of certain Bacillus subtilis strains, including isolates from spoiled food products, exhibit different germination behavior from spores of the well‐studied model organism Bacillus subtilis 168, often for unknown reasons. In this study, we analyzed spore germination efficiencies and kinetics of seventeen B. subtilis strains with previously sequenced genomes. A subsequent gene‐trait matching analysis revealed a correlation between a slow germination phenotype and the presence of a mobile genetic element, i.e., a Tn1546‐like transposon. A detailed investigation of the transposon elements showed an essential role of a specific operon (spoVA2mob) in inhibiting spore germination with nutrients and with the cationic surfactant dodecylamine. Our results indicate that this operon negatively influences release of Ca‐DPA by the SpoVA channel and may additionally alter earlier germination events, potentially by affecting proteins in the spore inner membrane. The spoVA2mob operon is an important factor that contributes to inter‐strain differences in spore germination. Screening for its genomic presence can be applied for identification of spores that exhibit specific properties that impede spore eradication by industrial processes.
Anaerobic microbial Fe(II) oxidation and Fe(III) reduction in coastal marine sediments controlled by organic carbon content
Authors: Laufer Katja , Byrne James M. , Glombitza Clemens , Schmidt Caroline , Jørgensen Bo Barker , Kappler Andreas 
Published: May 2016

SummaryCoastal marine sediments contain varying concentrations of iron, oxygen, nitrate and organic carbon. It is unknown how organic carbon content influences the activity of nitrate‐reducing and phototrophic Fe(II)‐oxidizers and microbial Fe‐redox cycling in such sediments. Therefore, microcosms were prepared with two coastal marine sediments (Kalø Vig and Norsminde Fjord at Aarhus Bay, Denmark) varying in TOC from 0.4 to 3.0 wt%. The microcosms were incubated under light/dark conditions with/without addition of nitrate and/or Fe(II). Although most probable number (MPN) counts of phototrophic Fe(II)‐oxidizers were five times lower in the low‐TOC sediment, phototrophic Fe(II) oxidation rates were higher compared with the high‐TOC sediment. Fe(III)‐amended microcosms showed that this lower net Fe(II) oxidation in the high‐TOC sediment is caused by concurrent bacterial Fe(III) reduction. In contrast, MPN counts of nitrate‐reducing Fe(II)‐oxidizers and net rates of nitrate‐reducing Fe(II) oxidation were comparable in low‐ and high‐TOC sediments. However, the ratio of nitratereduced:iron(II)oxidized was higher in the high‐TOC sediment, suggesting that a part of the nitrate was reduced by mixotrophic nitrate‐reducing Fe(II)‐oxidizers and chemoorganoheterotrophic nitrate‐reducers. Our results demonstrate that dynamic microbial Fe cycling occurs in these sediments and that the extent of Fe cycling is dependent on organic carbon content.
Prediction of bacterial associations with plants using a supervised machine‐learning approach
Authors: Martínez‐García Pedro Manuel , López‐Solanilla Emilia , Ramos Cayo , Rodríguez‐Palenzuela Pablo 
Published: May 2016

SummaryRecent scenarios of fresh produce contamination by human enteric pathogens have resulted in severe food‐borne outbreaks, and a new paradigm has emerged stating that some human‐associated bacteria can use plants as secondary hosts. As a consequence, there has been growing concern in the scientific community about these interactions that have not yet been elucidated. Since this is a relatively new area, there is a lack of strategies to address the problem of food‐borne illnesses due to the ingestion of fruits and vegetables. In the present study, we performed specific genome annotations to train a supervised machine‐learning model that allows for the identification of plant‐associated bacteria with a precision of ∼93%. The application of our method to approximately 9500 genomes predicted several unknown interactions between well‐known human pathogens and plants, and it also confirmed several cases for which evidence has been reported. We observed that factors involved in adhesion, the deconstruction of the plant cell wall and detoxifying activities were highlighted as the most predictive features. The application of our strategy to sequenced strains that are involved in food poisoning can be used as a primary screening tool to determine the possible causes of contaminations.