title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1042 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Long non-coding RNA LINC01234 regulates proliferation, migration and invasion via HIF-2α pathways in clear cell renal cell carcinoma cells link: https://peerj.com/articles/10149 last-modified: 2020-10-14 description: Long non-coding RNAs (lncRNAs) have been proved to have an important role in different malignancies including clear cell renal cell carcinoma (ccRCC). However, their role in disease progression is still not clear. The objective of the study was to identify lncRNA-based prognostic biomarkers and further to investigate the role of one lncRNA LINC01234 in progression of ccRCC cells. We found that six adverse prognostic lncRNA biomarkers including LINC01234 were identified in ccRCC patients by bioinformatic analysis using The Cancer Genome Atlas database. LINC01234 knockdown impaired cell proliferation, migration and invasion in vitro as compared to negative control. Furthermore, the epithelial-mesenchymal transition was inhibited after LINC01234 knockdown. Additionally, LINC01234 knockdown impaired hypoxia-inducible factor-2a (HIF-2α) pathways, including a suppression of the expression of HIF-2α, vascular endothelial growth factor A, epidermal growth factor receptor, c-Myc, Cyclin D1 and MET. Together, these datas showed that LINC01234 was likely to regulate the progression of ccRCC by HIF-2α pathways, and LINC01234 was both a promising prognostic biomarker and a potential therapeutic target for ccRCC. creator: Feilong Yang creator: Cheng Liu creator: Guojiang Zhao creator: Liyuan Ge creator: Yimeng Song creator: Zhigang Chen creator: Zhuo Liu creator: Kai Hong creator: Lulin Ma uri: https://doi.org/10.7717/peerj.10149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems link: https://peerj.com/articles/9732 last-modified: 2020-10-13 description: Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops. creator: Sigisfredo Garnica creator: Ronja Rosenstein creator: Max Emil Schön uri: https://doi.org/10.7717/peerj.9732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Garnica et al. title: Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat link: https://peerj.com/articles/9849 last-modified: 2020-10-13 description: The pathology of cerebrovascular disorders, such as hypertension, is associated with genetic changes and dysfunction of basilar artery smooth muscle cells (BASMCs). Long-term high-salt diets have been associated with the development of hypertension. However, the molecular mechanisms underlying salt-sensitive hypertension-induced BASMC modifications have not been well defined, especially at the level of variations in gene transcription. Here, we utilized high-throughput sequencing and subsequent signaling pathway analyses to find a two–fold change or greater upregulated expression of 203 transcripts and downregulated expression of 165 transcripts in BASMCs derived from rats fed a high-salt diet compared with those from control rats. These differentially expressed transcripts were enriched in pathways involved in cellular, morphological, and structural plasticity, autophagy, and endocrine regulation. These transcripts changes in the BASMCs derived from high-salt intake–induced hypertensive rats may provide critical information about multiple cellular processes and biological functions that occur during the development of cerebrovascular disorders and provide potential new targets to help control or block the development of hypertension. creator: Junhao Huang creator: Lesha Zhang creator: Yang Fang creator: Wan Jiang creator: Juan Du creator: Jinhang Zhu creator: Min Hu creator: Bing Shen uri: https://doi.org/10.7717/peerj.9849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports link: https://peerj.com/articles/9924 last-modified: 2020-10-13 description: BackgroundMany scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available. However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown. This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy.MethodsFrom each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis. Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals. Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy. Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy.ResultsOf the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies. Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no policy than health science journals (RRR, 2.73; 95% CI [1.05–7.14]). Commercial publishers were more likely to have a weak policy relative to no policy than non-commercial publishers (RRR, 7.87; 95% CI, [3.98–15.57]). Journals by publishers in Europe, including the majority of those located in the United Kingdom and the Netherlands, were more likely to have a strong data sharing policy than a weak policy (RRR, 2.99; 95% CI [1.85–4.81]).ConclusionsThese findings may account for the increase in commercial publishers’ engagement in data sharing and indicate that European national initiatives that encourage and mandate data sharing may influence the presence of a strong policy in the associated journals. Future research needs to explore the factors associated with varied degrees in the strength of a data sharing policy as well as more diverse characteristics of journals related to the policy strength. creator: Jihyun Kim creator: Soon Kim creator: Hye-Min Cho creator: Jae Hwa Chang creator: Soo Young Kim uri: https://doi.org/10.7717/peerj.9924 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kim et al. title: Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients link: https://peerj.com/articles/9995 last-modified: 2020-10-13 description: BackgroundWe used bioinformatic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays to investigate the association between plasma microRNAs (miRNAs) and stable warfarin dosage in a Chinese Han population.MethodsBioinformatics analysis was used to screen out potential warfarin dose-associated miRNAs. Three plasma miRNAs were validated in 99 samples by RT-qPCR. Kruskal–Wallis test and multivariate logistic regression were used to compare differences in plasma miRNAs expression levels between three warfarin dosage groups.ResultsThere were significant between-group differences among the three dose groups for hsa-miR-133b expression (p = 0.005), but we observed an “n-shaped” dose-dependent curve rather than a linear relationship. Expression levels of hsa-miR-24-3p (p = 0.475) and hsa-miR-1276 (p = 0.558) were not significantly different in the multivariate logistic regression.ConclusionmiRNAs have received extensive attention as ideal biomarkers and possible therapeutic targets for various diseases. However, they are not yet widely used in precision medicine. Our results indicate that hsa-miR-133b may be a possible reference factor for the warfarin dosage algorithm. These findings emphasize the importance of a comprehensive evaluation of complex relationships in warfarin dose prediction models and provide new avenues for future pharmacogenomics studies. creator: Li Zhao creator: Jin Wang creator: Shaoxin Shi creator: Yuan Wu creator: Jumei Liu creator: Shiwei He creator: Yue Zou creator: Huabin Xie creator: Shengxiang Ge creator: Huiming Ye uri: https://doi.org/10.7717/peerj.9995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils link: https://peerj.com/articles/10017 last-modified: 2020-10-13 description: Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels. creator: Raden Pramesa Narakusumo creator: Alexander Riedel creator: Joan Pons uri: https://doi.org/10.7717/peerj.10017 license: https://creativecommons.org/licenses/by-nc/4.0/ rights: ©2020 Narakusumo et al. title: Utilising one minute and four minute recovery when employing the resistance training contrast method does not negatively affect subsequent jump performance in the presence of concurrent training link: https://peerj.com/articles/10031 last-modified: 2020-10-13 description: BackgroundLittle is known about contrast training and post-activation performance enhancement (PAPE) in a same day concurrent training model. The aim of the current study was to examine the use of two short duration (1-min and 4-min) recovery periods on drop jump performance in same day concurrently trained athletes.MethodsTen professional Australian Rules footballers (age, 20.6 ± 1.9 yr; height, 184.8 ± 6.9 cm; body mass, 85.8 ± 8.4 kg) completed two resistance training sessions with different PAPE recovery durations; 1-min and 4-min, 1 h following a field-based endurance session. Baseline (pre) drop jumps were compared to post-test maximal drop jumps, performed after each set of three squats (where each participant was encouraged to lift as heavy as they could), to determine changes between 1-min and 4-min recovery periods. Data were analysed by fitting a mixed model (significance was set at P ≤ 0.05). Corrected Hedges’ g standardised effect sizes ±95% confidence limits were calculated using group means ± SDs.ResultsThere were no significant differences between baseline and experimental sets 1, 2 and 3 for reactive strength index (RSI), flight time, and total and relative impulse for either recovery duration. However, for contact time, 1-min baseline was significantly different from set 2 (mean difference; 95% CI [0.029; 0.000–0.057 s], P = 0.047, ES; 95% CI [−0.27; −1.20 to 0.66]). For RSI and flight time, 1-min was significantly higher than 4-min (RSI: 0.367; 0.091 to 0.642, P = 0.010, ES; 95% CI [0.52; −0.37 to 1.42]; flight time: 0.033; 0.003 to 0.063 s, P = 0.027, ES; 95% CI [0.86; −0.06 to 1.78]).DiscussionShort recovery periods of 1-min may be a time-efficient form of prescribing strength-power exercise in contrast loading schemes. Longer recovery periods do not appear to benefit immediate, subsequent performance. creator: Dean Ritchie creator: Justin W.L. Keogh creator: Peter Reaburn creator: Jonathan D. Bartlett uri: https://doi.org/10.7717/peerj.10031 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ritchie et al. title: Plastome structure and adaptive evolution of Calanthe s.l. species link: https://peerj.com/articles/10051 last-modified: 2020-10-13 description: Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants. creator: Yanqiong Chen creator: Hui Zhong creator: Yating Zhu creator: Yuanzhen Huang creator: Shasha Wu creator: Zhongjian Liu creator: Siren Lan creator: Junwen Zhai uri: https://doi.org/10.7717/peerj.10051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9 link: https://peerj.com/articles/10077 last-modified: 2020-10-13 description: Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×106 cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures. creator: Ruirui Meng creator: Chenchen Wang creator: Lihua Wang creator: Yanlong Liu creator: Qiuwen Zhan creator: Jiacheng Zheng creator: Jieqin Li uri: https://doi.org/10.7717/peerj.10077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Meng et al. title: Integrating multiple microarray dataset analysis and machine learning methods to reveal the key genes and regulatory mechanisms underlying human intervertebral disc degeneration link: https://peerj.com/articles/10120 last-modified: 2020-10-13 description: Intervertebral disc degeneration (IDD), a major cause of lower back pain, has multiple contributing factors including genetics, environment, age, and loading history. Bioinformatics analysis has been extensively used to identify diagnostic biomarkers and therapeutic targets for IDD diagnosis and treatment. However, multiple microarray dataset analysis and machine learning methods have not been integrated. In this study, we downloaded the mRNA, microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) expression profiles (GSE34095, GSE15227, GSE63492GSE116726, GSE56081 and GSE67566) associated with IDD from the GEO database. Using differential expression analysis and recursive feature elimination, we extracted four optimal feature genes. We then used the support vector machine (SVM) to make a classification model with the four optimal feature genes. The ROC curve was used to evaluate the model’s performance, and the expression profiles (GSE63492, GSE116726, GSE56081, and GSE67566) were used to construct a competitive endogenous RNA (ceRNA) regulatory network and explore the underlying mechanisms of the feature genes. We found that three miRNAs (hsa-miR-4728-5p, hsa-miR-5196-5p, and hsa-miR-185-5p) and three circRNAs (hsa_circRNA_100723, hsa_circRNA_104471, and hsa_circRNA_100750) were important regulators with more interactions than the other RNAs across the whole network. The expression level analysis of the three datasets revealed that BCAS4 and SCRG1 were key genes involved in IDD development. Ultimately, our study proposes a novel approach to determining reliable and effective targets in IDD diagnosis and treatment. creator: Hongze Chang creator: Xiaolong Yang creator: Kemin You creator: Mingwei Jiang creator: Feng Cai creator: Yan Zhang creator: Liang Liu creator: Hui Liu creator: Xiaodong Liu uri: https://doi.org/10.7717/peerj.10120 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chang et al.