title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1357 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: PEST sequences from a cactus dehydrin regulate its proteolytic degradation link: https://peerj.com/articles/6810 last-modified: 2019-05-14 description: Dehydrins (DHNs) are intrinsically disordered proteins expressed under cellular dehydration-related stresses. In this study, we identified potential proteolytic PEST sequences located at the central and C-terminal regions from the Opuntia streptacantha OpsDHN1 protein. In order to evaluate these PEST sequences as proteolytic tags, we generated a translational fusion with the GUS reporter protein and OpsDHN1 coding sequence. We found a GUS degradation effect in tobacco agro-infiltrated leaves and Arabidopsis transgenic lines that expressed the fusion GUS::OpsDHN1 full-length. Also, two additional translational fusions between OpsDHN1 protein fragments that include the central (GUS::PEST-1) or the C-terminal (GUS::PEST-2) PEST sequences were able to decrease the GUS activity, with PEST-2 showing the greatest reduction in GUS activity. GUS signal was abated when the OpsDHN1 fragment that includes both PEST sequences (GUS::PEST-1-2) were fused to GUS. Treatment with the MG132 proteasome inhibitor attenuated the PEST-mediated GUS degradation. Point mutations of phosphorylatable residues in PEST sequences reestablished GUS signal, hence these sequences are important during protein degradation. Finally, in silico analysis identified potential PEST sequences in other plant DHNs. This is the first study reporting presence of PEST motifs in dehydrins. creator: Adriana L. Salazar-Retana creator: Israel Maruri-López creator: Itzell E. Hernández-Sánchez creator: Alicia Becerra-Flora creator: María de la Luz Guerrero-González creator: Juan Francisco Jiménez-Bremont uri: https://doi.org/10.7717/peerj.6810 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Salazar-Retana et al. title: Exploring perceptions of meaningfulness in visual representations of bivariate relationships link: https://peerj.com/articles/6853 last-modified: 2019-05-14 description: Researchers often need to consider the practical significance of a relationship. For example, interpreting the magnitude of an effect size or establishing bounds in equivalence testing requires knowledge of the meaningfulness of a relationship. However, there has been little research exploring the degree of relationship among variables (e.g., correlation, mean difference) necessary for an association to be interpreted as meaningful or practically significant. In this study, we presented statistically trained and untrained participants with a collection of figures that displayed varying degrees of mean difference between groups or correlations among variables and participants indicated whether or not each relationship was meaningful. The results suggest that statistically trained and untrained participants differ in their qualification of a meaningful relationship, and that there is significant variability in how large a relationship must be before it is labeled meaningful. The results also shed some light on what degree of relationship is considered meaningful by individuals in a context-free setting. creator: Nataly Beribisky creator: Heather Davidson creator: Robert A. Cribbie uri: https://doi.org/10.7717/peerj.6853 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Beribisky et al. title: Functional analysis of the GbDWARF14 gene associated with branching development in cotton link: https://peerj.com/articles/6901 last-modified: 2019-05-14 description: Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements. creator: Ping Wang creator: Sai Zhang creator: Jing Qiao creator: Quan Sun creator: Qian Shi creator: Chaowei Cai creator: Jianchuan Mo creator: Zongyan Chu creator: Youlu Yuan creator: Xiongming Du creator: Yuchen Miao creator: Xiao Zhang creator: Yingfan Cai uri: https://doi.org/10.7717/peerj.6901 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: P5CR1 protein expression and the effect of gene-silencing on lung adenocarcinoma link: https://peerj.com/articles/6934 last-modified: 2019-05-14 description: The present study aimed to investigate the expression of pyrroline-5-carboxylate reductase 1 (P5CR1) protein in lung adenocarcinoma and paracancerous tissues and to explore the effect of silencing the encoding gene PYCR1 on the proliferation, migration, invasion, and cisplatin sensitivity in lung adenocarcinoma cells, thereby providing a novel therapeutic target for the treatment of the disease. Immunohistochemistry staining was used to detect the P5CR1 protein expression in lung adenocarcinoma and paracancerous tissues, and statistical analysis evaluated the correlation between P5CR1 protein expression and gender, age, tissue part, or pathological grade. The CCK8 assay was performed to detect the proliferation and cisplatin sensitivity, while the effect of PYCR1 on the migration and invasion of lung adenocarcinoma cells was detected by scratch test and transwell chamber assay. The findings demonstrated that the P5CR1 protein expression was significantly elevated in lung adenocarcinoma tissues and correlated with the pathological grade, whereas no significant correlation was established between the protein expression and gender, age, or tissue part. Furthermore, after PYCR1 gene silencing, the proliferation and invasion were significantly suppressed, while the sensitivity to cisplatin was significantly enhanced. Therefore, it can be speculated that the PYCR1 gene affects the biological behavior of lung adenocarcinoma and cisplatin resistance, serving as a potential therapeutic target for lung adenocarcinoma. creator: Yang She creator: Aiyou Mao creator: Feng Li creator: Xiaobin Wei uri: https://doi.org/10.7717/peerj.6934 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 She et al. title: Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis link: https://peerj.com/articles/6950 last-modified: 2019-05-14 description: Haemophilus parasuis is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among H. parasuis strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iron–sulphur cluster regulator (iscR)-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in H. parasuis. Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and iscR-based phylogeny was observed. It shows that iscR is a reliable marker for studying population structure of H. parasuis, while other factors should be included to avoid the interference of gene exchange of iscR between isolates. The two lineages of H. parasuis may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of H. parasuis, which helps understanding the extreme diversity within this pathogenic bacterium. creator: Junxing Li creator: Lihua Xu creator: Fei Su creator: Bin Yu creator: Xiufang Yuan uri: https://doi.org/10.7717/peerj.6950 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Alternative bait trials in the Barents Sea snow crab fishery link: https://peerj.com/articles/6874 last-modified: 2019-05-13 description: Commercial harvesting of snow crab (Chionoecetes opilio) in the Barents Sea started in 2012 by Norwegian fishing vessels. This new fishery has significant bait requirements, representing an emerging conservation challenge. In this study, we evaluate the performance of five alternative (natural) baits manufactured from the waste stream of existing and sustainably managed harp seal (Pagophilus groenlandicus) and minke whale (Balaenoptera acutorostrata) capture. Five different types of new bait were evaluated, including seal fat (SF), seal fat with skin (SFS), seal meat with bone (SMB), whale fat with skin (WFS), and whale meat with fat (WMF). A comparative fishing experiment was conducted onboard a commercial snow crab fishing vessel in the Barents Sea (May–June, 2016) to evaluate the performance of traditional bait (squid, Illexs spp.) and alternative baits at catching snow crabs. Performance of the different baits were compared on the basis of the number of commercial crab caught per trap haul catch per unit effort (CPUE) and carapace width (CW). Our results showed that SF and SFS performed equally well to traditional bait, with no statistical difference in CPUE (p-value = 0.325 and 0.069, respectively). All of the other experimental baits significantly decreased CPUE, when compared to squid. No significant effect of bait treatment on CW was detected and the cumulative distribution of CW was the same between control traps and each of the bait treatments. Overall the results indicated that SF and SFS represent a viable alternative to replace traditional bait, addressing a key conservation challenge in this bait intensive snow crab fishery. creator: Tomas Araya-Schmidt creator: Leonore Olsen creator: Lasse Rindahl creator: Roger B. Larsen creator: Paul D. Winger uri: https://doi.org/10.7717/peerj.6874 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Araya-Schmidt et al. title: The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast link: https://peerj.com/articles/6883 last-modified: 2019-05-13 description: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More information on its life cycle, dispersal mechanisms, and ecology are thus desirable. creator: Annette F. Govindarajan creator: Björn Källström creator: Erik Selander creator: Carina Östman creator: Thomas G. Dahlgren uri: https://doi.org/10.7717/peerj.6883 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Govindarajan et al.