title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1281 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers link: https://peerj.com/articles/7742 last-modified: 2019-09-20 description: Annual ryegrass (Lolium multiflorum) is a widely used cool-season turf and forage grass with high productivity and ornamental characteristics. However, the abundant intra-cultivar genetic variability usually hampers the application of conventional techniques for cultivar identification. The objectives of this study were to: (1) describe an efficient strategy for identification of six tetraploid annual ryegrass cultivars and (2) investigate the genetic diversity based on SSR markers. A total of 242 reliable bands were obtained from 29 SSR primer pairs with an average of 8.3 bands for each primer pair and the average value of polymorphic information content (PIC) was 0.304. The result of analysis of molecular variance (AMOVA) revealed that 81.99% of the genetic variation occurred in within-cultivars and 18.01% among-cultivars. The principal coordinate analysis (PCoA) showed that the first two principal axes explain 8.57% (PC1) and 6.05% (PC2) of total variation, respectively. By using multi-bulk strategy based on different filtering thresholds, the results suggested that bands frequency of 40% could be used as a reliable standard for cultivar identification in annual ryegrass. Under this threshold, 12 SSR primer pairs (00-04A, 02-06G, 02-08C, 03-05A, 04-05B, 10-09E, 12-01A, 13-02H, 13-12D, 14-06F, 15-01C and 17-10D) were detected for direct identification of six tetraploid annual ryegrass cultivars, which could be incorporated into conservation schemes to protect the intellectual property of breeders, ensure purity for consumers, as well as guarantee effective use of cultivars in future. creator: Gang Nie creator: Ting Huang creator: Xiao Ma creator: Linkai Huang creator: Yan Peng creator: Yanhong Yan creator: Zhou Li creator: Xia Wang creator: Xinquan Zhang uri: https://doi.org/10.7717/peerj.7742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nie et al. title: Curcumin plays a synergistic role in combination with HSV-TK/GCV in inhibiting growth of murine B16 melanoma cells and melanoma xenografts link: https://peerj.com/articles/7760 last-modified: 2019-09-20 description: Melanoma is a global concern and accounts for the major mortality of skin cancers. Herpes simplex virus thymidine kinase gene with ganciclovir (HSV-TK/GCV) is a promising gene therapy for melanoma. Despite its low efficiency, it is well known for its bystander effect which is mainly mediated by gap junction. In this study, we found that curcumin reduced B16 melanoma cell viability in both time- and dose-dependent manner. Further study showed that curcumin improved the gap junction intercellular communication (GJIC) function, and upregulated the proteins essential to gap junction, such as connexin 32 and connexin 43, indicating the potential role in enhancing the bystander effect of HSV-TK/GCV. By co-culturing the B16TK cells, which stably expressed TK gene, with wildtype B16 (B16WT) cells, we found that co-treatment of curcumin and GCV synergistically inhibited B16 cell proliferation, but the effect could be eliminated by the gap junction inhibitor AGA. Moreover, curcumin markedly increased apoptosis rate of B16WT cells, suggesting its effect in enhancing the bystander effect of HSV-TK/GCV. In the in-vivo study, we established the xenografted melanoma model in 14 days by injecting mixture of B16TK and B16WT cell in a ratio of 3:7. The result demonstrated that, co-administration of curcumin and GCV significantly inhibited the xenograft growth, as indicated by the smaller size and less weight. The combinational effect was further confirmed as a synergistic effect. In conclusion, the results demonstrated that curcumin could enhance the killing effect and the bystander effect of HSV-TK/GCV in treating melanoma, which might be mediated by improved gap junction. Our data suggested that combination of HSV-TK/GCV with curcumin could be a potential chemosensitization strategy for cancer treatment. creator: Hong Li creator: Haiyan Du creator: Guangxian Zhang creator: Yingya Wu creator: Pengxiang Qiu creator: Jingjing Liu creator: Jing Guo creator: Xijuan Liu creator: Lingling Sun creator: Biaoyan Du creator: Yuhui Tan uri: https://doi.org/10.7717/peerj.7760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Identification of pivotal lncRNAs in papillary thyroid cancer using lncRNA–mRNA–miRNA ceRNA network analysis link: https://peerj.com/articles/7441 last-modified: 2019-09-19 description: BackgroundTo identify pivotal lncRNAs in papillary thyroid cancer (PTC) using lncRNA–mRNA–miRNA ceRNA network analysis.MethodsWe obtained gene expression profiles from the gene expression omnibus database. Cancer specific lncRNA, cancer specific miRNA and cancer specific mRNA were identified. An integrated analysis was conducted to detect potential lncRNA–miRNA–mRNA ceRNA in regulating disease transformation. The lncRNA regulated gene ontology (GO) terms and regulated pathways were performed by function analysis. Survival analysis was performed for the pivotal lncRNAs.ResultsA total of four lncRNAs, 15 miRNAs and 375 mRNAs are identified as the key mediators in the pathophysiological processes of PTC. GO annotation enrichment analysis showed the most relevant GO terms are signal transduction, integral component of membrane and calcium ion binding. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed different changed genes mainly enriched in pathways in cancer, PI3K-Akt signaling pathway and focal adhesion. Among four lncRNAs, only SLC26A4-AS1 was significantly associated with PTC patient disease free survival.ConclusionThis study has constructed lncRNA–mRNA–miRNA ceRNA networks in PTC. The study provides a set of pivotal lncRNAs for future investigation into the molecular mechanisms. creator: Weiwei Liang creator: Fangfang Sun uri: https://doi.org/10.7717/peerj.7441 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liang and Sun title: Ankle and midtarsal joint quasi-stiffness during walking with added mass link: https://peerj.com/articles/7487 last-modified: 2019-09-19 description: Examination of how the ankle and midtarsal joints modulate stiffness in response to increased force demand will aid understanding of overall limb function and inform the development of bio-inspired assistive and robotic devices. The purpose of this study is to identify how ankle and midtarsal joint quasi-stiffness are affected by added body mass during over-ground walking. Healthy participants walked barefoot over-ground at 1.25 m/s wearing a weighted vest with 0%, 15% and 30% additional body mass. The effect of added mass was investigated on ankle and midtarsal joint range of motion (ROM), peak moment and quasi-stiffness. Joint quasi-stiffness was broken into two phases, dorsiflexion (DF) and plantarflexion (PF), representing approximately linear regions of their moment-angle curve. Added mass significantly increased ankle joint quasi-stiffness in DF (p < 0.001) and PF (p < 0.001), as well as midtarsal joint quasi-stiffness in DF (p < 0.006) and PF (p < 0.001). Notably, the midtarsal joint quasi-stiffness during DF was ~2.5 times higher than that of the ankle joint. The increase in midtarsal quasi-stiffness when walking with added mass could not be explained by the windlass mechanism, as the ROM of the metatarsophalangeal joints was not correlated with midtarsal joint quasi-stiffness (r = −0.142, p = 0.540). The likely source for the quasi-stiffness modulation may be from active foot muscles, however, future research is needed to confirm which anatomical structures (passive or active) contribute to the overall joint quasi-stiffness across locomotor tasks. creator: Andrew M. Kern creator: Nikolaos Papachatzis creator: Jeffrey M. Patterson creator: Dustin A. Bruening creator: Kota Z. Takahashi uri: https://doi.org/10.7717/peerj.7487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kern et al. title: Negative emotional state slows down movement speed: behavioral and neural evidence link: https://peerj.com/articles/7591 last-modified: 2019-09-19 description: BackgroundAthletic performance is affected by emotional state. Athletes may underperform in competition due to poor emotion regulation. Movement speed plays an important role in many competition events. Flexible control of movement speed is critical for effective athletic performance. Although behavioral evidence showed that negative emotion can influence movement speed, the nature of the relationship remains controversial. Thus, the present study investigated how negative emotion affects movement speed and the neural mechanism underlying the interaction between emotion processing and movement control.MethodsThe present study combined electroencephalography (EEG) technology with a cued-action task to investigate the effect of negative emotion on movement speed. In total, 21 undergraduate students were recruited for this study. Participants were asked to perform six consecutive action tasks after viewing an emotional picture. Pictures were presented in two blocks (one negative and one neutral). After the participants completed a set of tasks (neutral of negative), they were subjected to complete a 9-point self-assessment manikin scale. Participants underwent EEG while performing the tasks.ResultsAt the behavior level, there was a significant main effect of emotional valence on movement speed, with participants exhibiting significantly slower movements in the negative emotional condition than in the neutral condition. EEG data showed increased theta oscillation and larger P1 amplitude in response to negative than to neural images suggesting that more cognitive resources were required to process negative than neutral images. EEG data also showed a larger late CNV area in the neutral condition than in the negative condition, which suggested that there was a significant decrease in brain activation during action tasks in negative emotional condition than in the neural. While the early CNV did not reveal a significant main effect of emotional valence.ConclusionThe present results indicate that a negative emotion can slow movement, which is largely due to negative emotional processing consuming more resources than non-emotional processing and this interference effect mainly occurred in the late movement preparation phase. creator: Xiawen Li creator: Guanghui Zhang creator: Chenglin Zhou creator: Xiaochun Wang uri: https://doi.org/10.7717/peerj.7591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer link: https://peerj.com/articles/7602 last-modified: 2019-09-19 description: BackgroundRecent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC).MethodsHere we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs.ResultsIn this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found.ConclusionsOur findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets. creator: Wenliang Yuan creator: Sihua Peng creator: Jingyu Wang creator: Cai Wei creator: Zhen Ye creator: Ye Wang creator: Meiliang Wang creator: Hao Xu creator: Shouwen Jiang creator: Dan Sun creator: Chaoxu Dai creator: Linhua Jiang creator: Xiaobo Li uri: https://doi.org/10.7717/peerj.7602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yuan et al. title: A new record of kelp Lessonia spicata (Suhr) Santelices in the Sub-Antarctic Channels: implications for the conservation of the “huiro negro” in the Chilean coast link: https://peerj.com/articles/7610 last-modified: 2019-09-19 description: The Katalalixar National Reserve (KNR) lies in an isolated marine protected area of Magellan Sub-Antarctic channels, which represent an important area for marine biodiversity and macroalgal conservation. The present study is the first report of the species Lessonia spicata, “huiro negro”, in the Magellan Sub-Antarctic channels. This finding has implications for macroalgal biogeography and conservation concerns in the Chilean coast. In the ecological assessments of the KNR in 2018 we found populations of L. spicata, specifically on rocky shores of Torpedo Island and Castillo Channel. The morphological identification and molecular phylogeny based on nuclear (ITS1) sequences revealed that these populations of Lessonia are within the lineage of L. spicata of central Chile. This report increases the species richness of kelps for the Magellan Sub-Antarctic Channels from two to three confirmed species (L. flavicans, L. searlesiana and L. spicata), and it also extends the southern distribution range of L. spicata. This species has high harvest demand and is moving towards southern Chile; thus, these populations should be considered as essential for macroalgal conservation in high latitudes of South America. creator: Sebastián Rosenfeld creator: Fabio Mendez creator: Martha S. Calderon creator: Francisco Bahamonde creator: Juan Pablo Rodríguez creator: Jaime Ojeda creator: Johanna Marambio creator: Matthias Gorny creator: Andrés Mansilla uri: https://doi.org/10.7717/peerj.7610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosenfeld et al. title: Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau link: https://peerj.com/articles/7645 last-modified: 2019-09-19 description: The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP. creator: Li Ma creator: Shixiao Xu creator: Hongjin Liu creator: Tianwei Xu creator: Linyong Hu creator: Na Zhao creator: Xueping Han creator: Xiaoling Zhang uri: https://doi.org/10.7717/peerj.7645 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ma et al. title: Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae link: https://peerj.com/articles/7688 last-modified: 2019-09-19 description: A new istiodactylid pterosaur, Nurhachius luei sp. nov., is here reported based on a complete skull with mandible and some cervical vertebrae from the lower part of the Jiufotang Formation of western Liaoning (China). This is the second species of Nurhachius, the type-species being N. ignaciobritoi from the upper part of the Jiufotang Formation. A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species. The relationships within the Istiodactylidae and with their closest taxa are investigated through a phylogenetic analysis by parsimony. creator: Xuanyu Zhou creator: Rodrigo V. Pêgas creator: Maria E.C. Leal creator: Niels Bonde uri: https://doi.org/10.7717/peerj.7688 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhou et al. title: LC–MS/MS quantitative analysis of phylloquinone, menaquinone-4 and menaquinone-7 in the human serum of a healthy population link: https://peerj.com/articles/7695 last-modified: 2019-09-19 description: A novel application of the liquid chromatography method combined with the triple quadrupole tandem mass spectrometry method was developed for the quantification of vitamin K1 and two forms of vitamin K2 (menaquinone-4, menaquinone-7) in human serum. Total chromatography time for each run was 9 min. Time required for the sample pretreatment procedures was approximately 4 h. The coefficients of variation (CVs) of intra-assay were 10.4%, 3.2 % and 2.3% for vitamin K1 in three levels of quality control samples; were 14.3%, 3.2% and 6.7% for menaquinone-4; and were 11.1%, 6.0% and 7.0% for menaquinone-7. The inter-assay CVs were 12.8%, 11.3% and 7.4% for vitamin K1; were 15.2%, 9.2% and 8.7% for menaquinone-4; and were 13.2%,11.1% and 7.2% for menaquinone-7. No interference was found between K1, menaquinone-4 and menaquinone-7, nor any deuterated internal standards. This method was then used to determine reference values for Caucasian populations of central European origin. Samples were measured from 191 healthy volunteers (51.2 ± 16.2 years (mean ± SD)) and the values concerning K1 were 0.044–1.357 ng/mL for women and 0.030–1.214 ng/mL for men. The values for menaquinone-4 and menaquinone-7 did not exhibit any differences between women and men, and were 0.050–1.598 and 0.074–0.759 ng/mL, respectively. creator: Katerina Dunovska creator: Eva Klapkova creator: Bruno Sopko creator: Jana Cepova creator: Richard Prusa uri: https://doi.org/10.7717/peerj.7695 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dunovska et al.