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: Spatial and temporal variations of aridity shape dung beetle assemblages towards the Sahara desert link: https://peerj.com/articles/5210 last-modified: 2018-09-20 description: BackgroundAssemblage responses to environmental gradients are key to understand the general principles behind the assembly and functioning of communities. The spatially and temporally uneven distribution of water availability in drylands creates strong aridity gradients. While the effects of spatial variations of aridity are relatively well known, the influence of the highly-unpredictable seasonal and inter-annual precipitations on dryland communities has been seldom addressed.AimsHere, we study the seasonal and inter-annual responses of dung beetle (Coleoptera, Scarabaeidae) communities to the variations of water availability along a semiarid region of the Mediterranean.MethodsWe surveyed a 400 km linear transect along a strong aridity gradient from the Mediterranean coast to the Sahara (Eastern Morocco), during four sampling campaigns: two in the wet season and two in the dry season. We measured species richness, abundance and evenness. Variations in community composition between sites, seasons and years were assessed through beta diversity partitioning of dissimiliarity metrics based on species occurrences and abundances. The effects of climate, soil, vegetation and dung availability were evaluated using Spearman-rank correlations, general linear regressions and partial least-squares generalized linear regressions for community structure, and non-metric multi-dimensional scaling, Permutational Analysis of Variance (PERMANOVA) and distance-based RDA variation partitioning for compositional variations.ResultsDung beetle abundance and species richness showed large seasonal variations, but remained relatively similar between years. Indeed, aridity and its interaction with season and year were the strongest correlates of variations in species richness and composition. Increasing aridity resulted in decreasing species richness and an ordered replacement of species, namely the substitution of the Mediterranean fauna by desert assemblages dominated by saprophagous and generalist species both in space towards the Sahara and in the dry season.DiscussionOur study shows that aridity determines composition in dung beetle communities, filtering species both in space and time. Besides the expected decrease in species richness, such environmental filtering promotes a shift towards generalist and saprophagous species in arid conditions, probably related to changes in resource quality along the transect and through the year. Our results highlight the importance of considering the effects of the highly-unpredictable seasonal and inter-annual variations in precipitation when studying dryland communities. creator: Indradatta deCastro-Arrazola creator: Joaquín Hortal creator: Marco Moretti creator: Francisco Sánchez-Piñero uri: https://doi.org/10.7717/peerj.5210 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 deCastro-Arrazola et al. title: Inflammation-based prognostic scores predict the prognosis of locally advanced cervical esophageal squamous cell carcinoma patients receiving curative concurrent chemoradiotherapy: a propensity score-matched analysis link: https://peerj.com/articles/5655 last-modified: 2018-09-19 description: IntroductionThe present study investigated the crucial role of inflammation-based prognostic scores in locally advanced cervical esophageal squamous cell carcinoma (ESCC) patients who underwent curative concurrent chemoradiotherapy (CCRT).MethodsThere were 411 ESCC patients enrolled, including 63 cervical ESCC patients. Using the propensity score matching method, 63 thoracic ESCC patients were matched to the 63 cervical ESCC patients. The inflammation-based prognostic scores included the neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR), albumin level, c-reactive protein (CRP) level, modified Glasgow prognostic score (mGPS), and CRP/albumin ratio. The chi-square test and Kaplan–Meier method were used for categorical variable data and overall survival, respectively. A Cox regression model was performed for univariate and multivariable analyses.ResultsWith respect to cervical ESCC, NLR ≥ 2.5 (P = 0.019), PLR ≥ 103 (P = 0.013), CRP value >10 mg/l (P = 0.040), mGPS ≥ 1 (P = 0.040), and CRP/albumin ratio ≥ 9.5 (P = 0.033) were significant predictors of worse overall survival (OS) in the univariate analysis. In a multivariable analysis, PLR ≥ 103 (P = 0.010, HR: 2.66, 95% CI [1.27–5.58]) and mGPS ≥ 1 (P = 0.030, HR: 2.03, 95% CI [1.07–3.86]) were the independent prognostic parameters of worse OS. The prognostic value of these biomarkers in the matched thoracic ESCC patients was similar and compatible with the results in the cervical ESCC group in the univariate and multivariable analyses.ConclusionsOur study suggests that these inflammation-based prognostic scores are helpful in clinical practice, and PLR and mGPS may predict the prognosis for locally advanced cervical ESCC patients who receive curative CCRT. creator: Chia-Che Wu creator: Shau-Hsuan Li creator: Hung-I Lu creator: Chien-Ming Lo creator: Yu-Ming Wang creator: Shang-Yu Chou creator: Yen-Hao Chen uri: https://doi.org/10.7717/peerj.5655 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wu et al. title: Discovery of two skin-derived dermaseptins and design of a TAT-fusion analogue with broad-spectrum antimicrobial activity and low cytotoxicity on healthy cells link: https://peerj.com/articles/5635 last-modified: 2018-09-19 description: Two novel peptides belonging to the dermaseptin family, namely DRS-CA-1 and DRS-DU-1, were encoded from cDNA libraries derived from the skin secretions of Phyllomedusa camba and Callimedusa (Phyllomedusa) duellmani. Both natural peptides are highly-conserved and exhibited high potency against wild-type Gram-positive, Gram-negative bacteria, yeast and antibiotic-resistant bacteria (MRSA and Pseudomonas aeruginosa) (MICs 4–8 µM) with no obvious hemolytic activity. Collectively these results suggest that both peptides may have potential as novel antibiotics. Additionally, DRS-DU-1 exhibited selective cytotoxicity to tumor cells. The truncated analogue, DP-1 and TAT-fused DP-1 (namely DP-2) were subsequently synthesised. It showed that DP-1 had low antimicrobial activity, no hemolytic and cytotoxicity to tumor cells. However, DP-2 possessed strong antimicrobial activity and the similar selective, no obvious hemolytic activity and cytotoxicity on normal human cells, but enhanced cytotoxicity to tumor cells of DRS-DU-1. These findings indicate that the N-terminus of the dermaseptins may contribute to their bioactivity, and that addition of the TAT peptide can improve biological activity. The results provide a new insight for designing novel peptide-based antimicrobial or anticancer agents with low hemolytic activity and cytotoxicity. creator: Haohao Zhu creator: Xiyan Ding creator: Wei Li creator: Tulin Lu creator: Chengbang Ma creator: Xinping Xi creator: Lei Wang creator: Mei Zhou creator: Roberta Burden creator: Tianbao Chen uri: https://doi.org/10.7717/peerj.5635 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhu et al. title: Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions link: https://peerj.com/articles/5631 last-modified: 2018-09-19 description: The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species. creator: Haolong Wang creator: Haishen Wen creator: Yun Li creator: Kaiqiang Zhang creator: Yang Liu uri: https://doi.org/10.7717/peerj.5631 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: European population trends and current conservation status of an endangered steppe-bird species: the Dupont’s lark Chersophilus duponti link: https://peerj.com/articles/5627 last-modified: 2018-09-19 description: BackgroundSteppe-birds face drastic population declines throughout Europe. The Dupont’s lark Chersophilus duponti is an endangered steppe-bird species whose European distribution is restricted to Spain. This scarce passerine bird could be considered an ‘umbrella species’, since its population trends may reveal the conservation status of shrub-steppes. However, trends for the Spanish, and thus European, population of Dupont’s lark are unknown. In this work, we evaluated Dupont’s lark population trends in Europe employing the most recent and largest compiled database to date (92 populations over 12 years). In addition, we assessed the species threat category according to current applicable criteria (approved in March 2017) in the Spanish catalogue of threatened species (SCTS), which have never been applied to the Dupont’s lark nor to any other Spanish species. Finally, we compared the resulting threat categories with the current conservation status at European, national and regional levels.MethodsWe fitted switching linear trend models (software TRIM—Trends and Indices for Monitoring data) to evaluate population trends at national and regional scale (i.e. per Autonomous Community) during the period 2004–2015. In addition, the average finite annual rate of change ($\overline \lambda $λ¯) obtained from the TRIM analysis was employed to estimate the percentage of population size change in a 10-year period. A threat category was assigned following A1 and A2 criteria applicable in the SCTS.ResultsTrends showed an overall 3.9% annual decline rate for the Spanish population (moderate decline, following TRIM). Regional analyses showed high inter-regional variability. We forecasted a 32.8% average decline over the next 10 years. According to these results, the species should be listed as ‘Vulnerable’ at a national scale (SCTS). At the regional level, the conservation status of the species is of particular concern in Andalusia and Castile-Leon, where the species qualifies for listing as ‘Endangered’.DiscussionOur results highlight the concerning conservation status of the European Dupont’s lark population, undergoing a 3.9% annual decline rate. Under this scenario, the implementation of a wide-ranging conservation plan is urgently needed and is vital to ensuring the conservation of this steppe-bird species. The role of administrations in matters of nature protection and the cataloguing of endangered species is crucial to reverse declining population trends of this and other endangered taxa. creator: Julia Gómez-Catasús creator: Cristian Pérez-Granados creator: Adrián Barrero creator: Gerard Bota creator: David Giralt creator: Germán M. López-Iborra creator: David Serrano creator: Juan Traba uri: https://doi.org/10.7717/peerj.5627 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Gómez-Catasús et al. title: Potential changes in the distribution of Carnegiea gigantea under future scenarios link: https://peerj.com/articles/5623 last-modified: 2018-09-19 description: Over the last decades several studies have identified that the directional changes in climate induced by anthropogenic emissions of greenhouse gases are affecting the ecology of desert ecosystems. In the Southwest United States, the impacts of climate change to plant abundance and distribution have already been reported, including in the Sonoran Desert ecosystem, home of the iconic Saguaro (Carnegiea gigantea). Hence, there is an urgent need to assess the potential impacts of climate change on the saguaro. The goals of this study are to provide a map of actual habitat suitability (1), describe the relationships between abiotic predictors and the saguaro distribution at regional extents (2), and describe the potential effect of climate change on the spatial distribution of the saguaro (3). Species Distribution Modeling (SDM) was used to investigate the relationships between abiotic variables and the Saguaro distribution. SDMs were calibrated using presence records, 2,000 randomly-generated pseudo absences, and ten abiotic variables. Of these, annual precipitation and max temperature of the warmest month was found to have the greatest relative influence on saguaro distribution. SDMs indicated that 6.9% and 8.1% of the current suitable habitat is predicted to be lost by 2050 and 2070, respectively. Therefore, predicted changes in climate may result in a substantial contraction of the suitable habitat for saguaro over the next century. By identifying the drivers of saguaro distribution and assessing potential changes in habitat suitability due to climate change, this study will help practitioners to design more comprehensive strategies to conserve the saguaro in the face of climate change. creator: Fabio Albuquerque creator: Blas Benito creator: Miguel Ángel Macias Rodriguez creator: Caitlin Gray uri: https://doi.org/10.7717/peerj.5623 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Albuquerque et al. 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.