bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronobiology of interspecific interactions in a changing world
Authors: Kronfeld-Schor Noga , Visser Marcel E. , Salis Lucia , van Gils Jan A. 
Published: October 2017

Animals should time activities, such as foraging, migration and reproduction, as well as seasonal physiological adaptation, in a way that maximizes fitness. The fitness outcome of such activities depends largely on their interspecific interactions; the temporal overlap with other species determines when they should be active in order to maximize their encounters with food and to minimize their encounters with predators, competitors and parasites. To cope with the constantly changing, but predictable structure of the environment, organisms have evolved internal biological clocks, which are synchronized mainly by light, the most predictable and reliable environmental cue (but which can be masked by other variables), which enable them to anticipate and prepare for predicted changes in the timing of the species they interact with, on top of responding to them directly. Here, we review examples where the internal timing system is used to predict interspecific interactions, and how these interactions affect the internal timing system and activity patterns. We then ask how plastic these mechanisms are, how this plasticity differs between and within species and how this variability in plasticity affects interspecific interactions in a changing world, in which light, the major synchronizer of the biological clock, is no longer a reliable cue owing to the rapidly changing climate, the use of artificial light and urbanization.This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Timing as a sexually selected trait: the right mate at the right moment
Authors: Hau Michaela , Dominoni Davide , Casagrande Stefania , Buck C. Loren , Wagner Gabriela , Hazlerigg David , Greives Timothy , Hut Roelof A. 
Published: October 2017

Sexual selection favours the expression of traits in one sex that attract members of the opposite sex for mating. The nature of sexually selected traits such as vocalization, colour and ornamentation, their fitness benefits as well as their costs have received ample attention in field and laboratory studies. However, sexually selected traits may not always be expressed: coloration and ornaments often follow a seasonal pattern and behaviours may be displayed only at specific times of the day. Despite the widely recognized differences in the daily and seasonal timing of traits and their consequences for reproductive success, the actions of sexual selection on the temporal organization of traits has received only scant attention. Drawing on selected examples from bird and mammal studies, here we summarize the current evidence for the daily and seasonal timing of traits. We highlight that molecular advances in chronobiology have opened exciting new opportunities for identifying the genetic targets that sexual selection may act on to shape the timing of trait expression. Furthermore, known genetic links between daily and seasonal timing mechanisms lead to the hypothesis that selection on one timescale may simultaneously also affect the other. We emphasize that studies on the timing of sexual displays of both males and females from wild populations will be invaluable for understanding the nature of sexual selection and its potential to act on differences within and between the sexes in timing. Molecular approaches will be important for pinpointing genetic components of biological rhythms that are targeted by sexual selection, and to clarify whether these represent core or peripheral components of endogenous clocks. Finally, we call for a renewed integration of the fields of evolution, behavioural ecology and chronobiology to tackle the exciting question of how sexual selection contributes to the evolution of biological clocks.This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Seasonal reproductive tactics: annual timing and the capital-to-income breeder continuum
Authors: Williams Cory T. , Klaassen Marcel , Barnes Brian M. , Buck C. Loren , Arnold Walter , Giroud Sylvain , Vetter Sebastian G. , Ruf Thomas 
Published: October 2017

Tactics of resource use for reproduction are an important feature of life-history strategies. A distinction is made between ‘capital’ breeders, which finance reproduction using stored energy, and ‘income’ breeders, which pay for reproduction using concurrent energy intake. In reality, vertebrates use a continuum of capital-to-income tactics, and, for many species, the allocation of capital towards reproduction is a plastic trait. Here, we review how trophic interactions and the timing of life-history events are influenced by tactics of resource use in birds and mammals. We first examine how plasticity in the allocation of capital towards reproduction is linked to phenological flexibility via interactions between endocrine/neuroendocrine control systems and the sensory circuits that detect changes in endogenous state, and environmental cues. We then describe the ecological drivers of reproductive timing in species that vary in the degree to which they finance reproduction using capital. Capital can be used either as a mechanism to facilitate temporal synchrony between energy supply and demand or as a means of lessening the need for synchrony. Within many species, an individual's ability to cope with environmental change may be more tightly linked to plasticity in resource allocation than to absolute position on the capital-to-income breeder continuum.
This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Sleep research goes wild: new methods and approaches to investigate the ecology, evolution and functions of sleep
Authors: Rattenborg Niels C. , de la Iglesia Horacio O. , Kempenaers Bart , Lesku John A. , Meerlo Peter , Scriba Madeleine F. 
Published: October 2017

Despite being a prominent aspect of animal life, sleep and its functions remain poorly understood. As with any biological process, the functions of sleep can only be fully understood when examined in the ecological context in which they evolved. Owing to technological constraints, until recently, sleep has primarily been examined in the artificial laboratory environment. However, new tools are enabling researchers to study sleep behaviour and neurophysiology in the wild. Here, we summarize the various methods that have enabled sleep researchers to go wild, their strengths and weaknesses, and the discoveries resulting from these first steps outside the laboratory. The initial studies to ‘go wild’ have revealed a wealth of interindividual variation in sleep, and shown that sleep duration is not even fixed within an individual, but instead varies in response to an assortment of ecological demands. Determining the costs and benefits of this inter- and intraindividual variation in sleep may reveal clues to the functions of sleep. Perhaps the greatest surprise from these initial studies is that the reduction in neurobehavioural performance resulting from sleep loss demonstrated in the laboratory is not an obligatory outcome of reduced sleep in the wild.This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Timing avian long-distance migration: from internal clock mechanisms to global flights
Authors: Åkesson Susanne , Ilieva Mihaela , Karagicheva Julia , Rakhimberdiev Eldar , Tomotani Barbara , Helm Barbara 
Published: October 2017

Migratory birds regularly perform impressive long-distance flights, which are timed relative to the anticipated environmental resources at destination areas that can be several thousand kilometres away. Timely migration requires diverse strategies and adaptations that involve an intricate interplay between internal clock mechanisms and environmental conditions across the annual cycle. Here we review what challenges birds face during long migrations to keep track of time as they exploit geographically distant resources that may vary in availability and predictability, and summarize the clock mechanisms that enable them to succeed. We examine the following challenges: departing in time for spring and autumn migration, in anticipation of future environmental conditions; using clocks on the move, for example for orientation, navigation and stopover; strategies of adhering to, or adjusting, the time programme while fitting their activities into an annual cycle; and keeping pace with a world of rapidly changing environments. We then elaborate these themes by case studies representing long-distance migrating birds with different annual movement patterns and associated adaptations of their circannual programmes. We discuss the current knowledge on how endogenous migration programmes interact with external information across the annual cycle, how components of annual cycle programmes encode topography and range expansions, and how fitness may be affected when mismatches between timing and environmental conditions occur. Lastly, we outline open questions and propose future research directions.This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Marine biorhythms: bridging chronobiology and ecology
Authors: Bulla Martin , Oudman Thomas , Bijleveld Allert I. , Piersma Theunis , Kyriacou Charalambos P. 
Published: October 2017

Marine organisms adapt to complex temporal environments that include daily, tidal, semi-lunar, lunar and seasonal cycles. However, our understanding of marine biological rhythms and their underlying molecular basis is mainly confined to a few model organisms in rather simplistic laboratory settings. Here, we use new empirical data and recent examples of marine biorhythms to highlight how field ecologists and laboratory chronobiologists can complement each other's efforts. First, with continuous tracking of intertidal shorebirds in the field, we reveal individual differences in tidal and circadian foraging rhythms. Second, we demonstrate that shorebird species that spend 8–10 months in tidal environments rarely maintain such tidal or circadian rhythms during breeding, likely because of other, more pertinent, temporally structured, local ecological pressures such as predation or social environment. Finally, we use examples of initial findings from invertebrates (arthropods and polychaete worms) that are being developed as model species to study the molecular bases of lunar-related rhythms. These examples indicate that canonical circadian clock genes (i.e. the homologous clock genes identified in many higher organisms) may not be involved in lunar/tidal phenotypes. Together, our results and the examples we describe emphasize that linking field and laboratory studies is likely to generate a better ecological appreciation of lunar-related rhythms in the wild.
This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Keeping time without a spine: what can the insect clock teach us about seasonal adaptation?
Authors: Denlinger David L. , Hahn Daniel A. , Merlin Christine , Holzapfel Christina M. , Bradshaw William E. 
Published: October 2017

Seasonal change in daylength (photoperiod) is widely used by insects to regulate temporal patterns of development and behaviour, including the timing of diapause (dormancy) and migration. Flexibility of the photoperiodic response is critical for rapid shifts to new hosts, survival in the face of global climate change and to reproductive isolation. At the same time, the daily circadian clock is also essential for development, diapause and multiple behaviours, including correct flight orientation during long-distance migration. Although studied for decades, how these two critical biological timing mechanisms are integrated is poorly understood, in part because the core circadian clock genes are all transcription factors or regulators that are able to exert multiple effects throughout the genome. In this chapter, we discuss clocks in the wild from the perspective of diverse insect groups across eco-geographic contexts from the Antarctic to the tropical regions of Earth. Application of the expanding tool box of molecular techniques will lead us to distinguish universal from unique mechanisms underlying the evolution of circadian and photoperiodic timing, and their interaction across taxonomic and ecological contexts represented by insects.
This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
Authors: Kaiser Florian , Bittrich Sebastian , Salentin Sebastian , Leberecht Christoph , Haupt V. Joachim , Krautwurst Sarah , Schroeder Michael , Labudde Dirk 
Published: October 2017

AbstractThe origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes.Author summaryAminoacyl tRNA synthetases (aaRS) are primordial enzymes essential for interpretation and transfer of genetic information. Understanding the origin of the peculiarities observed with aaRS can explain what constituted the earliest life forms and how the genetic code was established. The increasing amount of experimentally determined three-dimensional structures of aaRS opens up new avenues for high-throughput analyses of molecular mechanisms. In this study, we present an exhaustive structural analysis of ATP binding motifs. We unveil an oppositional implementation of enzyme substrate binding in each aaRS Class. While Class I binds via interactions mediated by backbone hydrogen bonds, Class II uses a pair of arginine residues to establish salt bridges to its ATP ligand. We show how nature realized the binding of the same ligand species with completely different mechanisms. In addition, we demonstrate that sequence or even structure analysis for conserved residues may miss important functional aspects which can only be revealed by ligand interaction studies. Additionally, the placement of those key residues in the structure supports a popular hypothesis, which states that prototypic aaRS were once coded on complementary strands of the same gene.
Phencyclidine discoordinates hippocampal network activity but not place fields
Authors: Kao Hsin-Yi , Dvořák Dino , Park EunHye , Kenney Jana , Kelemen Eduard , Fenton André A 
Published: October 2017

ABSTRACTWe used the psychotomimetic phencyclidine (PCP) to investigate the relationships between cognitive behavior, coordinated neural network function and information processing within the hippocampus place cell system. We report in rats that PCP (5mg/kg i.p.) impairs a well-learned hippocampus-dependent place avoidance behavior in rats that requires cognitive control, even when PCP is injected directly into dorsal hippocampus. PCP increases 60-100 Hz medium gamma oscillations in hippocampus CA1 and these increases correlate with the cognitive impairment caused by systemic PCP administration. PCP discoordinates theta-modulated medium and slow gamma oscillations in CA1 local field potentials (LFP) such that medium gamma oscillations become more theta-organized than slow gamma oscillations. CA1 place cell firing fields are preserved under PCP but the drug discoordinates the sub-second temporal organization of discharge amongst place cells. This discoordination causes place cell ensemble representations of a familiar space to cease resembling pre-PCP representations, despite preserved place fields. These findings point to the cognitive impairments caused by PCP arising from neural discoordination. PCP disrupts the timing of discharge with respect to the sub-second timescales of theta and gamma oscillations in the LFP. Because these oscillations arise from local inhibitory synaptic activity, these findings point to excitation-inhibition discoordination as the root of PCP-induced cognitive impairment.SIGNIFICANCE STATEMENTHippocampal neural discharge is temporally coordinated on timescales of theta and gamma oscillations in the local field potential, and the discharge of a subset of pyramidal neurons called “place cells” is spatially organized such that discharge is restricted to locations called a cell’s “place field.” Because this temporal coordination and spatial discharge organization is thought to represent spatial knowledge, we used the psychotomimetic phencyclidine (PCP) to disrupt cognitive behavior and assess the importance of neural coordination and place fields for spatial cognition. PCP impaired the judicious use of spatial information and discoordinated hippocampal discharge, without disrupting firing fields. These findings dissociate place fields from spatial cognitive behavior and suggest that hippocampus discharge coordination is crucial to spatial cognition.
The geometry of the distance-decay of similarity in ecological communities
Authors: Ladau Joshua , Green Jessica L. , Pollard Katherine S. 
Published: October 2017

AbstractUnderstanding beta-diversity has strong implications for evaluating the extent of biodiversity and formulating effective conservation policy. Here, we show that the distance-decay relationship, an important measure of beta-diversity, follows a universal form which we call the piecewise quadratic model. To derive the piecewise quadratic model, we develop a new conceptual framework which is based on geometric probability and several key insights about the roles of study design (e.g., plot dimensions and spatial distributions). We fit the piecewise quadratic model to six empirical distance-decay relationships, spanning a range of taxa and spatial scales, including surveys of tropical vegetation, mammals, and amphibians. We find that the model predicts the functional form of the relationships extremely well, with coefficients of determination in excess of 0.95. Moreover, the model predicts a phase transition at distance scales where sample plots are overlapping, which we confirm empirically. Our framework and model provide a fundamental, quantitative link between distance-decay relationships and the shapes of ranges of taxa.
Landscape genomic prediction for restoration of aEucalyptusfoundation species under climate change
Authors: Supple Megan A. , Bragg Jason G. , Broadhurst Linda M. , Nicotra Adrienne B. , Byrne Margaret , Andrew Rose L. , Widdup Abigail , Aitken Nicola C. , Borevitz Justin O. 
Published: October 2017

AbstractAs species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions.Eucalyptus melliodorais a foundation species of a critically endangered community in Australia that is a target for restoration. We examined patterns of genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining gene flow up to 500 km and associations with environmental variables. Climate chamber studies revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Overall our results suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model toE. melliodorarestoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration.
Dissociating ego- and allocentric neglect after stroke: prevalence, laterality and outcome predictors
Authors: Demeyere Nele , Gillebert Celine R. 
Published: October 2017

AbstractVisuospatial neglect is a neuropsychological condition commonly experienced after stroke, whereby a patient is unable to attend to stimuli on their contralesional side. We aimed to investigate whether egocentric and allocentric neglect are functionally dissociable and differ in prevalence, laterality and outcome predictors. A consecutive sample of 366 acute stroke patients completed the Broken Hearts test from the Oxford Cognitive Screen. A subsample of 160 patients was followed up 6 months later. We evaluated the association between egocentric and allocentric neglect, contrasted the prevalence and severity of left-sided versus right-sided neglect, and determined the predictors of persistence versus recovery at follow up. Clinically, we found a double dissociation between ego- and allocentric neglect, with 50% of the neglect patients showing ‘only’ egocentric neglect and 25% ‘only’ allocentric neglect. Importantly, patients with only allocentric neglect did not demonstrate any egocentric spatial bias in the locations of the allocentric errors. Left-sided egocentric neglect was more prevalent and more severe than right-sided egocentric neglect, though right-sided neglect was still highly prevalent in the acute stroke sample (35%). Leftsided allocentric neglect was more severe but not more prevalent than right-sided allocentric neglect. Overall recovery of neglect was high: 81% of egocentric and 75% of allocentric neglect patients recovered. Severity of neglect was the only significant behavioural measure for predicting recovery at 6 months.
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Authors: Choudhury Nila Roy , Heikel Gregory , Trubitsyna Maryia , Kubik Peter , Nowak Jakub Stanislaw , Webb Shaun , Granneman Sander , Spanos Christos , Rappsilber Juri , Castello Alfredo , Michlewski Gracjan 
Published: October 2017

ABSTRACTTRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. Almost nothing is known about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. Here, we reveal that RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25’s endogenous RNA targets and protein binding partners. Finally, we show that the RNA-binding activity of TRIM25 is important for its ubiquitin ligase function. These results reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor for their biological functions.