title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1488 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Function matters: a review of terminological differences in applied and basic clicker training research link: https://peerj.com/articles/5621 last-modified: 2018-09-19 description: In clicker training, animal trainers pair a small device (a “clicker”) with a reward when teaching or maintaining responding. Animal trainers often assume clicker training is a “science-based” way to train animals. But, the few studies that have compared clicker training to a control have not provided evidence that adding a clicker is beneficial to training. This may be because research on clicker training has studied only one of several potential functions of the clicker stimulus that have been discussed by animal trainers. A systematic approach to researching the function of the clicker in clicker training would benefit from collaboration between applied and basic researchers. However, this will require that terminological differences between animal trainers and basic researchers are reconciled. This paper reviews the few studies that have compared clicker training to a control group and then discusses how trainers and basic researchers use the same terminology in functionally different ways—suggesting the empirical support for mechanisms underlying clicker training is less robust than previously assumed. These differences highlight many opportunities to answer basic and applied research questions relative to clicker training methods. Advancements in clicker training methods will benefit animal trainers who have been using clicker training for decades as well as applied practitioners who have extended clicker training to humans in educational and clinical settings. creator: Nicole R. Dorey creator: David J. Cox uri: https://doi.org/10.7717/peerj.5621 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dorey and Cox title: Foraging dynamics are associated with social status and context in mouse social hierarchies link: https://peerj.com/articles/5617 last-modified: 2018-09-19 description: Living in social hierarchies requires individuals to adapt their behavior and physiology. We have previously shown that male mice living in groups of 12 form linear and stable hierarchies with alpha males producing the highest daily level of major urinary proteins and urine. These findings suggest that maintaining alpha status in a social group requires higher food and water intake to generate energetic resources and produce more urine. To investigate whether social status affects eating and drinking behaviors, we measured the frequency of these behaviors in each individual mouse living in a social hierarchy with non-stop video recording for 24 h following the initiation of group housing and after social ranks were stabilized. We show alpha males eat and drink most frequently among all individuals in the hierarchy and had reduced quiescence of foraging both at the start of social housing and after hierarchies were established. Subdominants displayed a similar pattern of behavior following hierarchy formation relative to subordinates. The association strength of foraging behavior was negatively associated with that of agonistic behavior corrected for gregariousness (HWIG), suggesting animals modify foraging behavior to avoid others they engaged with aggressively. Overall, this study provides evidence that animals with different social status adapt their eating and drinking behaviors according to their physiological needs and current social environment. creator: Won Lee creator: Eilene Yang creator: James P. Curley uri: https://doi.org/10.7717/peerj.5617 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al. title: Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree link: https://peerj.com/articles/5606 last-modified: 2018-09-19 description: Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis. creator: Jun Zeng creator: Jie Chen creator: Yixuan Kou creator: Yujin Wang uri: https://doi.org/10.7717/peerj.5606 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zeng et al. title: The metabolic response of the Bradypus sloth to temperature link: https://peerj.com/articles/5600 last-modified: 2018-09-19 description: Poikilotherms and homeotherms have different, well-defined metabolic responses to ambient temperature (Ta), but both groups have high power costs at high temperatures. Sloths (Bradypus) are critically limited by rates of energy acquisition and it has previously been suggested that their unusual departure from homeothermy mitigates the associated costs. No studies, however, have examined how sloth body temperature and metabolic rate vary with Ta. Here we measured the oxygen consumption (VO2) of eight brown-throated sloths (B. variegatus) at variable Ta’s and found that VO2 indeed varied in an unusual manner with what appeared to be a reversal of the standard homeotherm pattern. Sloth VO2 increased with Ta, peaking in a metabolic plateau (nominal ‘thermally-active zone’ (TAZ)) before decreasing again at higher Ta values. We suggest that this pattern enables sloths to minimise energy expenditure over a wide range of conditions, which is likely to be crucial for survival in an animal that operates under severe energetic constraints. To our knowledge, this is the first evidence of a mammal provisionally invoking metabolic depression in response to increasing Ta’s, without entering into a state of torpor, aestivation or hibernation. creator: Rebecca Naomi Cliffe creator: David Michael Scantlebury creator: Sarah Jane Kennedy creator: Judy Avey-Arroyo creator: Daniel Mindich creator: Rory Paul Wilson uri: https://doi.org/10.7717/peerj.5600 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cliffe et al. title: Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus link: https://peerj.com/articles/5598 last-modified: 2018-09-19 description: Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9–CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway. creator: Jonathan I. Watkinson creator: Peter A. Bowerman creator: Kevin C. Crosby creator: Sherry B. Hildreth creator: Richard F. Helm creator: Brenda S.J. Winkel uri: https://doi.org/10.7717/peerj.5598 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Watkinson et al. title: Transkingdom network reveals bacterial players associated with cervical cancer gene expression program link: https://peerj.com/articles/5590 last-modified: 2018-09-19 description: Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause the disease. Chromosomal amplifications have been identified as a source of upregulation for cervical cancer driver genes but cannot fully explain increased expression of immune genes in invasive carcinoma. Insight into additional factors that may tip the balance from immune tolerance of HPV to the elimination of the virus may lead to better diagnosis markers. We investigated whether microbiota affect molecular pathways in cervical carcinogenesis by performing microbiome analysis via sequencing 16S rRNA in tumor biopsies from 121 patients. While we detected a large number of intra-tumor taxa (289 operational taxonomic units (OTUs)), we focused on the 38 most abundantly represented microbes. To search for microbes and host genes potentially involved in the interaction, we reconstructed a transkingdom network by integrating a previously discovered cervical cancer gene expression network with our bacterial co-abundance network and employed bipartite betweenness centrality. The top ranked microbes were represented by the families Bacillaceae, Halobacteriaceae, and Prevotellaceae. While we could not define the first two families to the species level, Prevotellaceae was assigned to Prevotella bivia. By co-culturing a cervical cancer cell line with P. bivia, we confirmed that three out of the ten top predicted genes in the transkingdom network (lysosomal associated membrane protein 3 (LAMP3), STAT1, TAP1), all regulators of immunological pathways, were upregulated by this microorganism. Therefore, we propose that intra-tumor microbiota may contribute to cervical carcinogenesis through the induction of immune response drivers, including the well-known cancer gene LAMP3. creator: Khiem Chi Lam creator: Dariia Vyshenska creator: Jialu Hu creator: Richard Rosario Rodrigues creator: Anja Nilsen creator: Ryszard A. Zielke creator: Nicholas Samuel Brown creator: Eva-Katrine Aarnes creator: Aleksandra E. Sikora creator: Natalia Shulzhenko creator: Heidi Lyng creator: Andrey Morgun uri: https://doi.org/10.7717/peerj.5590 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lam et al. title: A phylogenetic taxonomy of the Cyrtodactylus peguensis group (Reptilia: Squamata: Gekkonidae) with descriptions of two new species from Myanmar link: https://peerj.com/articles/5575 last-modified: 2018-09-19 description: A phylogenetic taxonomy of species in the Cyrtodactylus peguensis group from the Ayeyarwady Basin of Myanmar is constructed based on color pattern, morphology, and molecular systematic analyses using the mitochondrial gene NADH dehydrogenase subunit 2. Newly collected samples from the type locality of C. peguensis and other localities indicate that this clade is endemic to central Myanmar and contains at least seven species, four of which are undescribed. Three species, including C. peguensis occur in the low hills of the Bago Yoma Range within the central portion of the Ayeyarwady Basin. Two of these, C. myintkyawthurai sp. nov. from the northern and central Bago Yoma and C. meersi sp. nov. which is syntopic with C. peguensis in the southern Bago Yoma are described herein. As more lowland hilly areas bordering, and within the Ayeyarwady Basin are surveyed, more new species of this group are likely to be discovered. These discoveries continue the recent surge of descriptions of new species of Cyrtodactylus that are being discovered in Myanmar. creator: L. Lee Grismer creator: Perry L. Wood creator: Evan S.H. Quah creator: Matthew L. Murdoch creator: Marta S. Grismer creator: Mark W. Herr creator: Robert E. Espinoza creator: Rafe M. Brown creator: Aung Lin uri: https://doi.org/10.7717/peerj.5575 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Grismer et al. title: Colour vision of green turtle (Chelonia mydas) hatchlings: do they still prefer blue under water? link: https://peerj.com/articles/5572 last-modified: 2018-09-19 description: BackgroundSeveral anatomical studies provide evidence that green turtles (Chelonia mydas) possess the necessary anatomy for colour vision. Behavioural experiments have previously been conducted with newly emerged hatchlings, concluding that they are attracted to shorter wavelengths compared to longer wavelengths within a terrestrial environment, suggesting a possible attraction towards blue. This paper assessed the colour vision of hatchlings within an aquatic environment, and investigated whether the attraction for shorter wavelengths remains consistent within water, whether the colour saturation of the chromatic stimuli was an important factor, and whether rearing and testing individual animals in different coloured housing tanks has an impact on their visual choices.MethodsForty-one hatchling green turtles were presented with a three-choice experiment where food was attached to three different coloured plates. The plates (blue, yellow, and red) were randomly arranged in the turtle’s tank and four different colour saturations were tested (100, 75, 50, and 25%). Turtles were individually placed into their housing tanks (coloured either red, white, blue or grey) with three different colour plates in front of them, from the same saturation level. The colour of the plate with food first approached and bitten by the turtle was recorded.ResultsThe colour of the tank in which an individual was reared, and where experiments were conducted, significantly influenced which food item was selected on the different coloured plates. While individual turtles preferred to select the food items associated with blue plates across the entire experiment (66.1% of the time compared to 18.2% and 15.7% for yellow and red plates respectively), the preference for blue plates was influenced by the colour of the rearing/experimental tank. Individuals raised in red, white or blue tanks appeared to consistently prefer food on blue plates, but there appeared to be no plate colour preference by turtles in grey tanks. There was no significant effect of either colour saturation or the spatial arrangement of the three colours within an experimental tank on colour choice, and no significant interaction between tank colour and colour saturation.DiscussionThesefindings confirm that the terrestrial preference towards shorter wavelength colours, such as blue, compared to longer wavelength colours remains consistent within an aquatic environment. This preference for blue continues even as the colour saturation reduces from 100% down to 25%, and the colours become darker. Thus, it is suggested that green turtle hatchlings have a strong attraction towards blue. This attraction, however, is influenced by the colour of the tank the turtles were raised in. While this supports the notion that environmental colour may influence individual turtle visual capabilities, it suggests that this relationship is more complicated, and requires further investigation. creator: Rebecca Jehne Hall creator: Simon K.A. Robson creator: Ellen Ariel uri: https://doi.org/10.7717/peerj.5572 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hall et al. 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.