title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1485 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Population trend inferred from aural surveys for calling anurans in Korea link: https://peerj.com/articles/5568 last-modified: 2018-09-19 description: Amphibian populations fluctuate naturally in size and range and large datasets are required to establish trends in species dynamics. To determine population trends for the endangered Suweon Treefrog (Dryophytes suweonensis), we conducted aural surveys in 2015, 2016, and 2017 at each of 122 sites where the species was known to occur in the Republic of Korea. Despite being based on individual counts, the focus of this study was to establish population trends rather than population size estimates, and we found both environmental and landscape variables to be significant factors. Encroachment was also a key factor that influenced both the decreasing number of calling individuals and the negative population dynamics, represented here by the difference in the number of calling individuals between years. Generally, most sites displayed minimal differences in the number of calling males between years, although there was a large fluctuation in the number of individuals at some sites. Finally, when adjusted for the overall population size difference between years, we found the population size to be decreasing between 2015 and 2017, with a significant decrease in the number of calling individuals at specific sites. High rate of encroachment was the principal explanatory factor behind these marked negative peaks in population dynamics. creator: Amaël Borzée creator: Desiree Andersen creator: Yikweon Jang uri: https://doi.org/10.7717/peerj.5568 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Borzée et al. title: Parvalbumin expression and gamma oscillation occurrence increase over time in a neurodevelopmental model of NMDA receptor dysfunction link: https://peerj.com/articles/5543 last-modified: 2018-09-19 description: Dysfunction of the N-methyl-d-aspartate receptor (NMDAR) is thought to play a role in the pathophysiology of neurodevelopmental diseases like schizophrenia. To study the effects of NMDAR dysfunction on synaptic transmission and network oscillations, we used hippocampal tissue of NMDAR subunit GluN2A knockout (KO) mice. Field excitatory postsynaptic potentials were recorded in acute hippocampal slices of adult animals. Synaptic transmission was impaired in GluN2A KO slices compared to wild-type (WT) slices. Further, to investigate whether NMDAR dysfunction would alter neurodevelopment in vitro, we used organotypic hippocampal slice cultures of WT and GluN2A KO mice. Immunostaining performed with cultures kept two, seven, 14, 25 days in vitro (DIV) revealed an increasing expression of parvalbumin (PV) over time. As a functional readout, oscillatory activity induced by the cholinergic agonist carbachol was recorded in cultures kept seven, 13, and 26 DIV using microelectrode arrays. Initial analysis focused on the occurrence of delta, theta, beta and gamma oscillations over genotype, DIV and hippocampal area (CA1, CA3, dentate gyrus (DG)). In a follow-up analysis, we studied the peak frequency and the peak power of each of the four oscillation bands per condition. The occurrence of gamma oscillations displayed an increase by DIV similar to the PV immunostaining. Unlike gamma occurrence, delta, theta, and beta occurrence did not change over time in culture. The peak frequency and peak power in the different bands of the oscillations were not different in slices of WT and GluN2A KO mice. However, the level of PV expression was lower in GluN2A KO compared to WT mice. Given the role of PV-containing fast-spiking basket cells in generation of oscillations and the decreased PV expression in subjects with schizophrenia, the study of gamma oscillations in organotypic hippocampal slices represents a potentially valuable tool for the characterization of novel therapeutic drugs. creator: Ben van Lier creator: Andreas Hierlemann creator: Frédéric Knoflach uri: https://doi.org/10.7717/peerj.5543 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 van Lier et al. title: High definition video loggers provide new insights into behaviour, physiology, and the oceanic habitat of a marine predator, the yellow-eyed penguin link: https://peerj.com/articles/5459 last-modified: 2018-09-19 description: Camera loggers are increasingly used to examine behavioural aspects of free-ranging animals. However, often video loggers are deployed with a focus on specific behavioural traits utilizing small cameras with a limited field of view, poor light performance and video quality. Yet rapid developments in consumer electronics provide new devices with much improved visual data allowing a wider scope for studies employing this novel methodology. We developed a camera logger that records full HD video through a wide-angle lens, providing high resolution footage with a greater field of view than other camera loggers. The main goal was to assess the suitability of this type of camera for the analysis of various aspects of the foraging ecology of a marine predator, the yellow-eyed penguin in New Zealand. Frame-by-frame analysis allowed accurate timing of prey pursuits and time spent over certain seafloor types. The recorded video footage showed that prey species were associated with certain seafloor types, revealed different predator evasion strategies by benthic fishes, and highlighted varying energetic consequences for penguins pursuing certain types of prey. Other aspects that could be analysed were the timing of breathing intervals between dives and observe exhalation events during prey pursuits, a previously undescribed behaviour. Screen overlays facilitated analysis of flipper angles and beat frequencies throughout various stages of the dive cycle. Flipper movement analysis confirmed decreasing effort during descent phases as the bird gained depth, and that ascent was principally passive. Breathing episodes between dives were short (<1 s) while the majority of the time was devoted to subsurface scanning with a submerged head. Video data recorded on free-ranging animals not only provide a wealth of information recorded from a single deployment but also necessitate new approaches with regards to analysis of visual data. Here, we demonstrate the diversity of information that can be gleaned from video logger data, if devices with high video resolution and wide field of view are utilized. creator: Thomas Mattern creator: Michael D. McPherson creator: Ursula Ellenberg creator: Yolanda van Heezik creator: Philipp J. Seddon uri: https://doi.org/10.7717/peerj.5459 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mattern et al. title: Neural processing of working memory in adults with ADHD in a visuospatial change detection task with distractors link: https://peerj.com/articles/5601 last-modified: 2018-09-18 description: Individuals with Attention-Deficit Hyperactivity Disorder (ADHD) are often characterized by deficits in working memory (WM), which manifest in academic, professional, and mental health difficulties. To better understand the underlying mechanisms of these presumed WM deficits, we compared adults with ADHD to their peers on behavioral and neural indices of WM. We used a visuospatial change detection task with distractors which was designed to assess the brain’s ability to effectively filter out distractors from WM, in addition to testing for effects of WM load. Twenty-seven unmedicated adults with ADHD were compared to 27 matched peers on event-related potential (ERP) measures of WM, i.e., the contralateral delay activity (CDA). Despite severe impairments in everyday life functioning, findings showed no difference in deficits in behavioral tests of working memory for adults with ADHD compared to their peers. Interestingly, there were differences in neural activity between individuals with ADHD and their peers showing that the CDA of individuals with ADHD did not distinguish between high, distractor, and low memory load conditions. These data suggest, in the face of comparable behavioral performance, a difference in neural processing efficiency, wherein the brains of individuals with ADHD may not be as selective in the allocation of neural resources to perform a WM task. creator: Chao Gu creator: Zhong-Xu Liu creator: Rosemary Tannock creator: Steven Woltering uri: https://doi.org/10.7717/peerj.5601 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gu et al. title: Local-scale determinants of arboreal spider beta diversity in a temperate forest: roles of tree architecture, spatial distance, and dispersal capacity link: https://peerj.com/articles/5596 last-modified: 2018-09-18 description: Spiders are a functionally important taxon in forest ecosystems, but the determinants of arboreal spider beta diversity are poorly understood at the local scale. We examined spider assemblages in 324 European beech (Fagus sylvatica) trees of varying sizes across three forest stands in Würzburg (Germany) to disentangle the roles of tree architecture, spatial distance, and dispersal capacity on spider turnover across individual trees. A large proportion of tree pairs (66%) showed higher compositional dissimilarity in spider assemblages than expected by chance, suggesting prominent roles of habitat specialization and/or dispersal limitation. Trees with higher dissimilarity in DBH and canopy volume, and to a lesser extent in foliage cover, supported more dissimilar spider assemblages, suggesting that tree architecture comprised a relevant environmental gradient of sorting spider species. Variation partitioning revealed that 28.4% of the variation in beta diversity was jointly explained by tree architecture, spatial distance (measured by principal coordinates of neighbor matrices) and dispersal capacity (quantified by ballooning propensity). Among these, dispersal capacity accounted for a comparable proportion as spatial distance did (6.8% vs. 5.9%). Beta diversity did not significantly differ between high- and low-vagility groups, but beta diversity in species with high vagility was more strongly determined by spatially structured environmental variation. Altogether, both niche specialization, along the environmental gradient defined by tree architecture, and dispersal limitation are responsible for structuring arboreal spider assemblages. High dispersal capacity of spiders appears to reinforce the role of niche-related processes. creator: Qiongdao Zhang creator: Dong He creator: Hua Wu creator: Wei Shi creator: Cong Chen uri: https://doi.org/10.7717/peerj.5596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria link: https://peerj.com/articles/5593 last-modified: 2018-09-18 description: Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research. creator: Beata Śmietanka creator: Marek Lubośny creator: Aleksandra Przyłucka creator: Karin Gérard creator: Artur Burzyński uri: https://doi.org/10.7717/peerj.5593 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Śmietanka et al. title: Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses link: https://peerj.com/articles/5560 last-modified: 2018-09-18 description: BackgroundThe unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs.MethodsThe phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses.ResultsNo spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years.DiscussionThe comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers. creator: Alice Ferrari creator: Fausto Tinti creator: Victoria Bertucci Maresca creator: Alessandro Velonà creator: Rita Cannas creator: Ioannis Thasitis creator: Filipe Oliveira Costa creator: Maria Cristina Follesa creator: Daniel Golani creator: Farid Hemida creator: Sarah J. Helyar creator: Cecilia Mancusi creator: Antonello Mulas creator: Fabrizio Serena creator: Letizia Sion creator: Marco Stagioni creator: Alessia Cariani uri: https://doi.org/10.7717/peerj.5560 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ferrari et al. title: Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts link: https://peerj.com/articles/5302 last-modified: 2018-09-18 description: Male cuckoos Cuculus canorus produce calls that differ in number of syllables depending on environmental conditions and presence of male and female conspecifics. Why different males produce so repeatable calls that vary greatly in duration among males remains an open question. We used playback of cuckoo calls with few or many syllables (hereafter short and long calls), and woodpigeon calls (a control that also produces few or many syllables), predicting that playback of longer cuckoo calls should attract more male cuckoos (if males with such calls are dominant and successfully out-compete other males due to intraspecific competition), and attract more hosts mobbing male cuckoos (cuckoos with such calls and their females attract more hosts because of an increased risk of parasitism). Because cuckoos differentially parasitize hosts away from human habitation, we also tested whether the number of syllables in cuckoo calls differed with distance from buildings. Playback showed significant effects of number of syllables in cuckoo calls, but not woodpigeon Columba palumbus calls, with an additional effect of distance from human habitation decreasing the response to playback. These findings are consistent with the hypothesis that longer cuckoo calls, especially played back near human habitation, attract more conspecifics and hosts than shorter calls. To the best of knowledge this is the first study showing that cuckoo call response modified both other cuckoo individuals, as well as hosts response. creator: Piotr Tryjanowski creator: Federico Morelli creator: Tomasz S. Osiejuk creator: Anders Pape Møller uri: https://doi.org/10.7717/peerj.5302 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tryjanowski et al. title: Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center link: https://peerj.com/articles/5665 last-modified: 2018-09-17 description: PurposeMost studies on neuroblastoma (NB) have been conducted in Western countries or Japan. The objective of our study was to analyze clinical and pathological features, MYCN status, surgical methods, and prognosis in Chinese NB patients.MethodsA retrospective, single-center case series study of 275 NBs was implemented. Clinical manifestations, pathological features, MYCN status, and surgical treatment were analyzed. Log-rank test and Cox hazards models were used to assess overall survivals (OSs).ResultsThe cohort consisted of 105 females and 170 males, with an age range of five days to 15 years. MYCN amplification was detected in 21.5% of all cases. The median OS was 15.0 months for MYCN amplified group. The five-year OS rates were 70.8% and 18.3% for MYCN unamplified and amplified groups, respectively, and the comparison of Kaplan–Meier curves for these two groups showed statistical significance (P < .001 by log-rank test). Gross total resection (GTR, n = 111) and subtotal resection (STR, n = 58) were administered in 169 patients at stages 3 and 4 who received chemotherapy and the comparison of Kaplan–Meier curves for different groups in these patients had statistical significance (STR vs. GTR, P = .009; MYCN unamplified vs. amplified, P < .001 by log-rank test, respectively).The multivariate survival analyses showed statistical significance (STR vs. GTR, P = .047; MYCN unamplified vs. amplified, P = .001 by Cox regression model).ConclusionsMYCN amplification is an independently adverse prognostic factor in Chinese NB patients at stages 3 and 4 and GTR is associated with improved OS compared with STR in these patients. creator: Yangyang Ma creator: Jicui Zheng creator: Jiayan Feng creator: Lian Chen creator: Kuiran Dong creator: Xianmin Xiao uri: https://doi.org/10.7717/peerj.5665 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ma et al. title: 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3 link: https://peerj.com/articles/5620 last-modified: 2018-09-17 description: The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome. creator: Sergey Levitskii creator: Ksenia Derbikova creator: Maria V. Baleva creator: Anton Kuzmenko creator: Andrey V. Golovin creator: Ivan Chicherin creator: Igor A. Krasheninnikov creator: Piotr Kamenski uri: https://doi.org/10.7717/peerj.5620 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Levitskii et al.