title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1352 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions link: https://peerj.com/articles/6888 last-modified: 2019-05-15 description: BackgroundPoa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region.MethodsIn the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations.ResultsiPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula.DiscussionThe lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu’s FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic variation was surprisingly high, despite the observed significant traces of bottleneck/founder effect following demographic expansion, and was similar to that observed in populations from Poland and the Balkans. For the Antarctic population, the multiple introduction events from different sources are considered to be responsible for such an observation. Moreover, the results of STRUCTURE and PCoA showed that the P. annua from Antarctica has the highest genetic similarity to populations from Europe.ConclusionsThe observed polymorphism should be considered as a consequence of the joint influence of external abiotic stress and the selection process. Environmental changes, due to their ability to induce transposon activation, lead to the acceleration of evolutionary processes through the production of genetic variability. creator: Piotr Androsiuk creator: Justyna Koc creator: Katarzyna Joanna Chwedorzewska creator: Ryszard Górecki creator: Irena Giełwanowska uri: https://doi.org/10.7717/peerj.6888 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Androsiuk et al. title: Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae link: https://peerj.com/articles/6899 last-modified: 2019-05-15 description: BackgroundChlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa.MethodsWe sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae.ResultsConcatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome.DiscussionWhile the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions. creator: Karolina Fučíková creator: Paul O. Lewis creator: Suman Neupane creator: Kenneth G. Karol creator: Louise A. Lewis uri: https://doi.org/10.7717/peerj.6899 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fučíková et al. title: Development and feasibility study of an app (Ladle) for weight loss and behaviour change link: https://peerj.com/articles/6907 last-modified: 2019-05-15 description: BackgroundWeight management interventions involving behaviour change often utilise face to face interventions which include evidence based behaviour change strategies yet are costly and time intensive. In contrast, digital interventions cost less and have a wider reach yet tend to lack an evidence base and are less effective.AimsThe present study therefore aimed to develop an evidence based behaviour change low cost app for weight management and to provide a preliminary analysis of its effectiveness.MethodsThe Ladle app was developed through evidence review and feedback from health care professionals and patients and consists of a 12 week course focusing on six habits and weight loss facilitated through 36 audio psychological lessons and 12 lessons specifically on the six habits. Each lesson was between 2–5 min (approx. 168 min of lessons). It was evaluated in terms of completion rate, weight loss, adoption of the six habits and participant feedback.ResultsThe results showed a completion rate of 44%, that 52% of Completers showed weight loss of at least 5%, 79% showed weight loss of at least 3%, the median % weight lost was −5% and the median weight loss was −3.8 kg. Further, by the end of 12 weeks the majority (>80%) of participants had adopted four of the six habits for at least 5 days a week and nearly half (45%) had adopted the remaining two habits for at least 4 days out of 7. Feedback comments were mainly positive (n = 80) focusing mostly on the content of the lessons. Some comments were neutral (n = 56) and involved a statement of commitment or a description of a challenge and a minority were negative (n = 23) describing some technical issues which were addressed as the evaluation progressed.ConclusionThe new Ladle app offers an evidenced based alternative to more intensive face to face interventions. On preliminary analysis it would seem to have lower completion rates than some more intensive interventions but comparable effectiveness for weight loss. It can also improve habits and is less time-intensive and costly to deliver. Participant feedback was generally positive. creator: Jane Ogden creator: Hazel Maxwell creator: Adrian Wong uri: https://doi.org/10.7717/peerj.6907 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ogden et al. title: The Equidae from Cooper’s D, an early Pleistocene fossil locality in Gauteng, South Africa link: https://peerj.com/articles/6909 last-modified: 2019-05-15 description: Cooper’s D is a fossil locality in the Bloubank Valley close to other important sites such as Sterkfontein and Kromdraai in Gauteng, South Africa. The fossil deposits of Cooper’s D date to 1.38 ± 0.11 Ma. Hominins like Paranthropus robustus and early Homo have been recovered from Cooper’s Cave. We report here on the Equidae remains. Our sample contains specimens from the extinct Equus capensis, and a specimen which represents an extinct hipparion Eurygnathohippus cf. cornelianus. This particular specimen was previously identified as plains zebra (Equus quagga). The contribution of Equidae to the total fossil assemblage of Cooper’s D is relatively low, and these remains were likely accumulated by various predators such as spotted and brown hyenas and leopards. The Equidae, as well as the other fauna from Cooper’s D supports the existence of grassland, wooded and water components in the vicinity of the site. creator: Shaw Badenhorst creator: Christine M. Steininger uri: https://doi.org/10.7717/peerj.6909 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Badenhorst and Steininger title: The effect of differential spatiotopic information on the acquisition and generalization of fear of movement-related pain link: https://peerj.com/articles/6913 last-modified: 2019-05-15 description: Fear of movement-related pain significantly contributes to musculoskeletal chronic pain disability. Previous research has shown that fear of movement-related pain can be classically conditioned. That is, in a differential fear conditioning paradigm, after (repeatedly) pairing a neutral joystick movement (conditioned stimulus; CS+) with a painful stimulus (unconditioned stimulus; pain-US), that movement in itself starts to elicit self-reported fear and elevated psychophysiological arousal compared to a control joystick movement (CS−) that was never paired with pain. Further, it has been demonstrated that novel movements that are more similar to the original CS+ elicit more fear than novel movements that are more similar to the CS−, an adaptive process referred to as stimulus generalization. By default, movement/action takes place in reference to the three-dimensional space: a movement thus not only involves proprioceptive information, but it also contains spatiotopic information. Therefore, the aim of this study was to investigate to what extent spatiotopic information (i.e., endpoint location of movement) contributes to the acquisition and generalization of such fear of movement-related pain besides proprioception (i.e., movement direction). In a between-subjects design, the location group performed joystick movements from the middle position to left and right; the movement group moved the joystick from left and right to the middle. One movement (CS+) was paired with pain, another not (CS−). Feature overlap between CSs typically reduces differential learning. The endpoint of both CSs in the movement group is an overlapping feature whereas in the location group the endpoint of both CSs is distinct; therefore we hypothesized that there would be less differential fear learning in the movement group compared to the location group. We also tested generalization to movements with similar proprioceptive features but different endpoint location. Following the principle of stimulus generalization, we expected that novel movements in the same direction as the CS+ but with a different endpoint would elicit more fear than novel movement in the same direction of the CS− but with a different endpoint. Main outcome variables were self-reported fear and pain-US expectancy and eyeblink startle responses (electromyographic). Corroborating the feature overlap hypothesis, the location group showed greater differential fear acquisition. Fear generalization emerged for both groups in the verbal ratings, suggesting that fear indeed accrued to proprioceptive CS features; these effects, however, were not replicated in the startle measures. creator: Ann Meulders creator: Johan W. Vlaeyen uri: https://doi.org/10.7717/peerj.6913 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Meulders and Vlaeyen title: Effects of water level fluctuation on thermal stratification in a typical tributary bay of Three Gorges Reservoir, China link: https://peerj.com/articles/6925 last-modified: 2019-05-15 description: Xiangxi River is a typical tributary of Three Gorges Reservoir (TGR) in China. Based on field observations in 2010, thermal stratification was significant in most months of the year. Through field data analysis and numerical simulations, the seasonal and spatial variation of thermal stratification as related to the impact of the operation of TGR were investigated. Thermal stratification was most pronounced from April to September in the Xiangxi River tributary. Air temperature (AT) and water level (WL) were the two dominant variables impacting thermal stratification. AT affected the surface water temperature promoting the formation of thermal stratification, and high WLs in TGR deepened the thermocline depth and thermocline bottom depth. These results provide a preliminary description of the seasonal variation and spatial distribution of thermal stratification, which is important for better understanding how thermal stratification affects algae blooms in Xiangxi River. creator: Juxiang Jin creator: Scott A. Wells creator: Defu Liu creator: Guolu Yang creator: Senlin Zhu creator: Jun Ma creator: Zhengjian Yang uri: https://doi.org/10.7717/peerj.6925 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jin et al. title: Ellipse packing in two-dimensional cell tessellation: a theoretical explanation for Lewis’s law and Aboav-Weaire’s law link: https://peerj.com/articles/6933 last-modified: 2019-05-15 description: BackgroundLewis’s law and Aboav-Weaire’s law are two fundamental laws used to describe the topology of two-dimensional (2D) structures; however, their theoretical bases remain unclear.MethodsWe used R software with the Conicfit package to fit ellipses based on the geometric parameters of polygonal cells of ten different kinds of natural and artificial 2D structures.ResultsOur results indicated that the cells could be classified as an ellipse’s inscribed polygon (EIP) and that they tended to form the ellipse’s maximal inscribed polygon (EMIP). This phenomenon was named as ellipse packing. On the basis of the number of cell edges, cell area, and semi-axes of fitted ellipses, we derived and verified new relations of Lewis’s law and Aboav-Weaire’s law.ConclusionsEllipse packing is a short-range order that places restrictions on the cell topology and growth pattern. Lewis’s law and Aboav-Weaire’s law mainly reflect the effect of deformation from circle to ellipse on cell area and the edge number of neighboring cells, respectively. The results of this study could be used to simulate the dynamics of cell topology during growth. creator: Kai Xu uri: https://doi.org/10.7717/peerj.6933 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu title: Transcriptional regulation of Bcl-2 gene by the PR/SET domain family member PRDM10 link: https://peerj.com/articles/6941 last-modified: 2019-05-15 description: Bcl-2 (B-cell lymphoma 2) protein is localized in the outer membrane of mitochondria, where it plays an important role in promoting cellular survival and inhibiting the actions of pro-apoptotic proteins. PRDM10 is a member of the PR/SET family of epigenetic regulators and may play a role in development and cell differentiation. Here we show that human PRDM10 contributes to the transcriptional regulation of human Bcl-2 gene. We found that PRDM10-depletion in human cells reduced the expression of Bcl-2 protein and over-expression of PRDM10 promoted Bcl-2 protein expression. Furthermore, luciferase reporter activity of Bcl-2 gene P1 promoter was significantly increased in cells co-transfected with PRDM10, and PRDM10 was able to bind to the Bcl-2 P1 promoter in vivo. Using The Cancer Genome Atlas (TCGA) data set, we found weak positive correlation between PRDM10 and Bcl-2 in several cancer types including cancers of the breast, colon, and lung tissues. These data identify a novel function for PRDM10 protein and provide insights on the transcriptional control of Bcl-2 expression. creator: Na Chen creator: Taobo Hu creator: Yuanyuan Gui creator: Jieying Gao creator: Zhihong Li creator: Shi Huang uri: https://doi.org/10.7717/peerj.6941 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Effect of music interventions on anxiety during labor: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/6945 last-modified: 2019-05-15 description: BackgroundAnxiety is commonly experienced during the delivery process and has shown to have adverse effects on maternal and infant health outcomes. Music interventions tend to reduce the effects of anxiety in diverse populations, are low cost, are easily accessible, and have high acceptability. The aim of this review and meta-analysis was to assess the effectiveness of music interventions in reducing anxiety levels among women during labor.MethodsSeven databases from inception to the end of December, 2018, without any language or time restriction including Embase, PubMed, the Cochrane Library, the Cumulative Index to Nursing and Allied Health, PsycINFO, Airiti Library, and PerioPath: Index to Taiwan Periodical Literature were searched using key terms related to pregnancy, anxiety, and music. Randomized controlled trials that assessed the effect of music during labor and measured anxiety levels as an outcome were included. Meta-analyses were conducted to assess anxiety reduction following a music intervention compared to that after placebo treatment.ResultsA total of 14 studies that investigated a total of 1,310 participants were included in this review. The meta-analyses indicated that those in the intervention group had a significant decrease in anxiety scores (standardized mean difference = −2.40, 95% confidence interval (CI) [−3.29 to −1.52], p < 0.001; I2 = 97.66%), heart rate (HR) (difference in means = −3.04 beats/min, 95% CI [−4.79 to −1.29] beats/min, p = 0.001; I2 = 0.00%), systolic blood pressure (SBP) (difference in means = −3.71 mmHg, 95% CI [−7.07 to −0.35] mmHg, p = 0.031; I2 = 58.47%), and diastolic blood pressure (DBP) (difference in means = −3.54 mmHg, 95% CI [−5.27 to −1.81] mmHg, p < 0.001; I2 = 0.00%) as compared to the women in the control group.ConclusionsMusic interventions may decrease anxiety scores and physiological indexes related to anxiety (HR, SBP, and DBP). Music interventions may be a good non-pharmacological approach for decreasing anxiety levels during labor. creator: Hsin-Hui Lin creator: Yu-Chen Chang creator: Hsiao-Hui Chou creator: Chih-Po Chang creator: Ming-Yuan Huang creator: Shu-Jung Liu creator: Chin-Han Tsai creator: Wei-Te Lei creator: Tzu-Lin Yeh uri: https://doi.org/10.7717/peerj.6945 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lin et al. title: Clarifying a trophic black box: stable isotope analysis reveals unexpected dietary variation in the Peruvian anchovy Engraulis ringens link: https://peerj.com/articles/6968 last-modified: 2019-05-15 description: BackgroundSmall fishes play fundamental roles in pelagic ecosystems, channelling energy and nutrients from primary producers to higher trophic levels. They support globally important fisheries in eastern boundary current ecosystems like the Humboldt Current System (HCS) of the SE Pacific (Chile and Peru), where fish catches are the highest in the world (per unit area). This production is associated with coastal upwelling where fisheries target small pelagic fishes including the Peruvian anchovy (Engraulis ringens). The elevated biomass attained by small pelagics is thought to reflect their low trophic position in short/simple food chains. Despite their global importance, large gaps exist in our understanding of the basic ecology of these resources. For instance, there is an ongoing debate regarding the relative importance of phytoplankton versus animal prey in anchovy diet, and ecosystem models typically assign them a trophic position (TP) of ∼2, assuming they largely consume phytoplankton. Recent work based on both relative energetic content and stable isotope analysis (SIA) suggests that this value is too low, with δ15N values indicating that anchovy TP is ca. 3.5 in the Peruvian HCS.MethodsWe characterised the trophic ecology of adult anchovies (n = 30), their putative prey and carnivorous jack mackerel (n = 20) captured from N Chile. SIA (δ13C and δ15N) was used to estimate the relative contribution of different putative prey resources. δ15N was used to estimate population level trophic position.ResultsAnchovies showed little variability in δ13C (−18.7 to −16.1‰) but varied greatly in δ15N (13.8 to 22.8‰)—individuals formed two groups with low or high δ15N values. When considered as a single group, mixing models indicated that anchovy diet was largely composed of zooplankton (median contribution: 95% credibility limits), with major contributions of crustacean larvae (0.61: 0.37–0.77) and anchovy (preflexion) larvae (0.15: 0.02–0.34), and the assimilation of phytoplankton was negligible (0.05: 0–0.22). The modal (95% credibility limits) estimate of TP for the pooled anchovy sample was 3.23 (2.93–3.58), overlapping with recent SIA-based estimates from Peru. When the two δ15N groups were analysed separately, our results indicate that the lower δ15N group largely assimilated materials from crustacean larvae (0.73: 0.42–0.88), with a TP of 2.91 (2.62–3.23). Mixing models suggested high δ15N anchovies were cannibalistic, consuming anchovy preflexion larvae (0.55: 0.11–0.74). A carnivorous trophic niche was supported by high TP (3.79: 3.48–4.16), mirroring that of carnivorous juvenile jack mackerel (Trachurus murphyi; 3.80: 3.51–4.14). Our results support recent conclusions regarding high TP values of anchovy from Peru and reveal new insights into their trophic behaviour. These results also highlight the existence of cryptic trophic complexity and ecosystem function in pelagic food webs, classically considered as simple. creator: Jessica Pizarro creator: Felipe Docmac creator: Chris Harrod uri: https://doi.org/10.7717/peerj.6968 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pizarro et al.