title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=653 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: DDX17 modulates the expression and alternative splicing of genes involved in apoptosis and proliferation in lung adenocarcinoma cells link: https://peerj.com/articles/13895 last-modified: 2022-09-21 description: BackgroundThe DEAD-box RNA-binding protein (RBP) DDX17 has been found to be involved in the tumorigenesis of many types of cancers. However, the role of DDX17 in lung adenocarcinoma (LUAD) remains unclear.MethodsWe silenced DDX17 expression in A549 LUAD cells by small interfering RNA (siRNA). Cell proliferation and apoptosis assays were performed to explore the functions of DDX17. Knockdown of DDX17 by siRNA significantly inhibited proliferation and induced apoptosis in A549 cells. We used high-throughput RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) and alternative splicing (AS) events in DDX17 knockdown LUAD cells.ResultsDDX17 knockdown increased the expression levels of proapoptotic genes and decreased those of proproliferative genes. Moreover, the DDX17-regulated AS events in A549 cells revealed by computational analysis using ABLas software were strongly validated by quantitative reverse transcription–polymerase chain reaction (RT–qPCR) and were also validated by analysis of The Cancer Genome Atlas (TCGA)-LUAD dataset. These findings suggest that DDX17 may function as an oncogene by regulating both the expression and AS of proliferation- and apoptosis-associated genes in LUAD cells. Our findings may offer new insights into understanding the molecular mechanisms of LUAD and provide a new therapeutic direction for LUAD. creator: Cheng He creator: Gan Zhang creator: Yanhong Lu creator: Jingyue Zhou creator: Zixue Ren uri: https://doi.org/10.7717/peerj.13895 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: Exploring the trends of adaptation and evolution of sclerites with regards to habitat depth in sea pens link: https://peerj.com/articles/13929 last-modified: 2022-09-21 description: Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO3) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species, but a lack of information on sea pens has limited studies on their adaptation and evolution across depth. Here, we aimed to reveal trends of adaptation and evolution of sclerite shapes in sea pens with regards to habitat depth via phylogenetic analyses and ancestral reconstruction analyses. Colony form of sea pens is suggested to have undergone convergent evolution and the loss of axis has occurred independently across the evolution of sea pens. Divergences of sea pen taxa and of sclerite forms are suggested to depend on habitat depths. In addition, their sclerite forms may be related to evolutionary history of the sclerite and the surrounding chemical environment as well as water temperature. Three-flanged sclerites may possess the tolerance towards the environment of the deep sea, while plate sclerites are suggested to be adapted towards shallower waters, and have evolved independently multiple times. The common ancestor form of sea pens was predicted to be deep-sea and similar to family Pseudumbellulidae in form, possessing sclerites intermediate in form to those of alcyonaceans and modern sea pens such as spindles, rods with spines, and three-flanged sclerites with serrated edges sclerites, as well as having an axis and bilateral traits. creator: Yuka Kushida creator: Yukimitsu Imahara creator: Hin Boo Wee creator: Iria Fernandez-Silva creator: Jane Fromont creator: Oliver Gomez creator: Nerida Wilson creator: Taeko Kimura creator: Shinji Tsuchida creator: Yoshihiro Fujiwara creator: Takuo Higashiji creator: Hiroaki Nakano creator: Hisanori Kohtsuka creator: Akira Iguchi creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.13929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kushida et al. title: Trans-Arctic vicariance in Strongylocentrotus sea urchins link: https://peerj.com/articles/13930 last-modified: 2022-09-21 description: The sea urchins Strongylocentotus pallidus and S. droebachiensis first invaded the Atlantic Ocean from the Pacific following the opening of the Bering seaway in the late Miocene. While trans-Arctic dispersal during the Pleistocene is thought to have maintained species’ integrity, a recent genomic analysis identified a reproductively isolated cryptic species within S. droebachiensis. Based on previous studies, the distribution of one of these lineages (S. droebachiensis W) includes the shallow water habitats of the northwest Atlantic and Pacific, while the other (S. droebachiensis E) is found throughout the shallow habitat in the northeast but is mostly restricted to deep habitats (>65 m) in the northwest Atlantic. However, since genetic variation within S. droebachiensis has been largely unstudied in the north Pacific and Arctic oceans, the biogeography of the cryptic species is not well known, and it is difficult to identify the mechanisms driving population subdivision and speciation. Here we use population genetic analyses to characterize the distribution of each species, and to test hypotheses about the role of vicariance in the evolution of systematic and genomic divergence within the genus. We collected individuals of all three Strongylocentrotus species (n = 365) from 10 previously unsampled locations in the northeast Pacific and north Atlantic (Labrador Sea and Norway), and generated mtDNA sequence data for a 418 bp fragment of cytochrome c oxidase subunit I (COI). To assess the biogeography of all three species, we combined our alignment with five previously published data sets (total n = 789) and used statistical parsimony and maximum likelihood to identify species and characterize their distribution within and among oceans. Patterns of haplotype sharing, pairwise FST, and hierarchical analyses of molecular variance (AMOVA) identified trans-Arctic dispersal in S. pallidus and S. droebachiensis W, but other than 5 previously reported singletons we failed to detect additional mtDNA haplotypes of S. droebachiensis E in the north Pacific. Within the Atlantic, patterns of habitat segregation suggests that temperature may play a role in limiting the distribution of S. droebachiensis E, particularly throughout the warmer coastal waters along the coast of Nova Scotia. Our results are consistent with the cycles of trans-Arctic dispersal and vicariance in S. pallidus and S. droebachiensis W, but we suggest that the evolution of Atlantic populations of S. droebachiensis E has been driven by persistent trans-Arctic vicariance that may date to the initial invasion in the late Pliocene. creator: Jason A. Addison creator: Jinhong Kim uri: https://doi.org/10.7717/peerj.13930 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Addison and Kim title: RNA sequencing-based identification of microRNAs in the antler cartilage of Gansu red deer (Cervus elaphus kansuensis) link: https://peerj.com/articles/13947 last-modified: 2022-09-21 description: BackgroundThe velvet antler is a complex mammalian bone organ with unique biological characteristics, such as regeneration. The rapid growth stage (RGS) is a special period in the regeneration process of velvet antler.MethodsTo elucidate the functions of microRNAs (miRNAs) at the RGS of antler development in Gansu red deer (Cervus elaphus kansuensis), we used RNA sequencing (RNA-seq) to analyze miRNA expression profiles in cartilage tissues of deer antler tips at three different growth stages.ResultsThe RNA-seq results revealed 1,073 known and 204 novel miRNAs, including 1,207, 1,242, and 1,204 from 30-, 60-, and 90-d antler cartilage tissues, respectively. To identify key miRNAs controlling rapid antler growth, we predicted target genes of screened 25 differentially expressed miRNAs (DEMs) and specifically expressed miRNAs (SEMs) in 60 d and annotated their functions. The KEGG results revealed that target genes of 25 DEMs and 30 SEMs were highly classified in the “Metabolic pathways”, “Pathways in cancer”, “Proteoglycans in cancer” and “PI3K-Akt signaling pathway”. In addition, a novel miRNA (CM008039.1_315920), highly enriched in “NF-kappa B signaling pathway”, may need further study.ConclusionsThe miRNAs identified in our study are potentially important in rapid antler growth. Our findings provide new insights to help elucidate the miRNA-mediated regulatory mechanisms involved during velvet antler development in C. elaphus kansuensis. creator: Yanxia Chen creator: Zhenxiang Zhang creator: Jingjing Zhang creator: Xiaxia Chen creator: Yuqin Guo creator: Changzhong Li uri: https://doi.org/10.7717/peerj.13947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: IRF7-deficient MDCK cell based on CRISPR/Cas9 technology for enhancing influenza virus replication and improving vaccine production link: https://peerj.com/articles/13989 last-modified: 2022-09-21 description: The influenza virus is a cause of seasonal epidemic disease and enormous economic injury. The best way to control influenza outbreaks is through vaccination. The Madin-Darby canine kidney cell line (MDCK) is currently approved to manufacture influenza vaccines. However, the viral load from cell-based production is limited by host interferons (IFN). Interferon regulating factor 7 (IRF7) is a transcription factor for type-I IFN that plays an important role in regulating the anti-viral mechanism and eliminating viruses. We developed IRF7 knock-out MDCK cells (IRF7−/ − MDCK) using CRISPR/Cas9 technology. The RNA expression levels of IRF7 in the IRF7−/ − MDCK cells were reduced by 94.76% and 95.22% under the uninfected and infected conditions, respectively. Furthermore, the IRF7 protein level was also significantly lower in IRF7−/ − MDCK cells for both uninfected (54.85% reduction) and viral infected conditions (32.27% reduction) compared to WT MDCK. The differential expression analysis of IFN-related genes demonstrated that the IRF7−/ − MDCK cell had a lower interferon response than wildtype MDCK under the influenza-infected condition. Gene ontology revealed down-regulation of the defense response against virus and IFN-gamma production in IRF7−/ − MDCK. The evaluation of influenza viral titers by RT-qPCR and hemagglutination assay (HA) revealed IRF7−/ − MDCK cells had higher viral titers in cell supernatant, including A/pH1N1 (4 to 5-fold) and B/Yamagata (2-fold). Therefore, the IRF7−/ − MDCK cells could be applied to cell-based influenza vaccine production with higher capacity and efficiency. creator: Oraphan Mayuramart creator: Witthaya Poomipak creator: Somruthai Rattanaburi creator: Kritsada Khongnomnan creator: Songtham Anuntakarun creator: Suthat Saengchoowong creator: Tanit Chavalit creator: Naphat Chantaravisoot creator: Sunchai Payungporn uri: https://doi.org/10.7717/peerj.13989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mayuramart et al. title: Identification and expression profile analysis of the SnRK2 gene family in cucumber link: https://peerj.com/articles/13994 last-modified: 2022-09-21 description: The sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific type of serine/threonine protein kinase that plays an important role in the physiological regulation of stress. The objective of this study was to identify and analyze the members of the SnRK2 gene family in cucumber and lay a foundation for further exploration of the mechanism of CsSnRK2 resistance to stress. Here, 12 SnRK2 genes were isolated from cucumber and distributed on five chromosomes, phylogenetic clustering divided these into three well-supported clades. In addition, collinearity analysis showed that the CsSnRK2 gene family underwent purifying selection pressure during evolution. CsSnRK2 genes of the same group have similar exons and conserved motifs, and intron length may be a specific imprint for the evolutionary amplification of the CsSnRK2 gene family. By predicting cis elements in the promoter, we found that the promoter region of CsSnRK2 gene members had various cis-regulatory elements in response to hormones and stress. Relative expression analysis showed that CsSnRK2.11 (group II) and CsSnRK2.12 (group III) were strongly induced by ABA, NaCl and PEG stress; whereas CsSnRK2.2 (group III) was not activated by any treatment. The response of group I CsSnRK2 to ABA, NaCl and PEG was weak. Furthermore, protein interaction prediction showed that multiple CsSnRK2 proteins interacted with four proteins including protein phosphatase 2C (PP2C), and it is speculated that the CsSnRK2 genes may also an independent role as a third messenger in the ABA signaling pathway. This study provides a reference for analyzing the potential function of CsSnRK2 genes in the future research. creator: Zilong Wan creator: Shilei Luo creator: Zeyu Zhang creator: Zeci Liu creator: Yali Qiao creator: Xueqin Gao creator: Jihua Yu creator: Guobin Zhang uri: https://doi.org/10.7717/peerj.13994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wan et al. title: Effect of ZnO and CuO nanoparticles on the growth, nutrient absorption, and potential health risk of the seasonal vegetable Medicago polymorpha L. link: https://peerj.com/articles/14038 last-modified: 2022-09-21 description: BackgroundMedicago polymorpha L., a seasonal vegetable, is commonly grown in China. The increasing use of nanoparticles (NPs) such as ZnO and CuO NPs in agriculture has raised concerns about their potential risks for plant growth and for human consumption. There is a lack of research on the effects of ZnO and CuO NPs on agronomic performance of Medicago polymorpha L. and their potential risks for human health.MethodsIn this study, different treatment concentrations of ZnO NPs (25, 50, 100, and 200 mg kg−1) and CuO NPs (10, 25, 50, and 100 mg kg−1) were used to determine their effects on the growth and nutrient absorption of Medicago polymorpha L., as well as their potential risk for human health.ResultsThe results showed that ZnO and CuO NPs increased the fresh weight of Medicago polymorpha L. by 5.8–11.8 and 3.7–8.1%, respectively. The best performance for ZnO NPs occurred between 25–50 mg kg−1 and the best performance for CuO NPs occurred between 10–25 mg kg−1. Compared with the control, ZnO and CuO NPs improved the macronutrients phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). The following micronutrients were also improved: iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), and manganese (Mn), with the exception of nitrogen (N) accumulation. Low treatment concentrations exhibited more efficient nutrient uptake than high treatment concentrations. A comprehensive analysis showed that the optimum concentrations were 25 mg kg−1 for ZnO NPs and 10 mg kg−1 for CuO NPs. The potential non-carcinogenic health risk of Medicago polymorpha L. treated with ZnO and CuO NPs was analyzed according to the estimated daily intake (EDI), the hazard quotient (HQ), and the cumulative hazard quotient (CHQ). Compared with the oral reference dose, the EDI under different ZnO and CuO NPs treatments was lower. The HQ and CHQ under different ZnO and CuO NPs treatments were far below 1. This indicated that Medicago polymorpha L. treated with ZnO and CuO NPs did not pose any non-carcinogenic health risk to the human body. Therefore, ZnO and CuO NPs were considered as a safe nano fertilizer for Medicago polymorpha L. production according to growth analysis and a human health risk assessment. creator: Hongting Ji creator: Zhi Guo creator: Guodong Wang creator: Xin Wang creator: Hongjiang Liu uri: https://doi.org/10.7717/peerj.14038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ji et al. title: Physiological and biochemical responses of hybrid maize (Zea mays L.) varieties grown under heat stress conditions link: https://peerj.com/articles/14141 last-modified: 2022-09-21 description: Maize (Zea mays L.) is the second most commonly produced and consumed crop after wheat globally and is adversely affected by high heat, which is a significant abiotic stress factor. This study was carried out to determine the physiological and biochemical responses of hybrid corn varieties under heat stress (‘HS’) compared to control (‘C’) conditions during the 2020 and 2021 growing seasons. The experiment was conducted under natural conditions in the Southeastern region of Turkey, where the most intense temperatures are experienced. This experiment used split plots in randomized blocks with three replications, with ‘HS’ and ‘C’ growing conditions applied to the main plots and the different hybrid corn varieties (FAO 650) planted on the sub plots. Mean values of days to 50% tasseling (DT, day), grain yield (GY, kg ha−1), leaf water potential (LWP, %), chlorophyll-a (Chl-a, mg g−1), cell membrane damage (CMD, %), and total phenol content (TPC, μg g−1) were significantly different between years, growing conditions, and hybrid corn varieties. Changes in the climate played a significant role in the differences between the years and growing conditions (GC), while the genetic characteristics of the different corn varieties explained the differences in outcomes between them. The values of DT, GY, LWP, Chl-a, CMD, and TPC ranged from 49.06–53.15 days, 9,173.0–10,807.2 kg ha−1, 78.62–83.57%, 6.47–8.62 mg g−1, 9.61–13.54%, and 232.36–247.01 μg g−1, respectively. Significant correlations were recorded between all the parameters. Positive correlations were observed between all the variables except for CMD. The increased damage to cell membranes under ‘HS’ caused a decrease in the other measured variables, especially GY. In contrast, the GY increased with decreased CMD. CMD was important in determining the stress and tolerance level of corn varieties under ‘HS’ conditions. The GY and other physiological parameters of ADA 17.4 and SYM-307 candidate corn varieties surpassed the control hybrid corn cultivars. The results revealed that the ADA 17.4 and SYM-307 cultivars might have ‘HS’-tolerate genes. creator: Timucin Tas uri: https://doi.org/10.7717/peerj.14141 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tas title: High metabolic load distance in professional soccer according to competitive level and playing positions link: https://peerj.com/articles/13318 last-modified: 2022-09-20 description: BackgroundHigh metabolic load distance provides global information about the soccer players’ total high-intensity activities. Thus, this study aimed to examine the Spanish professional soccer players’ high metabolic load distance profile, comparing competitive level and playing positions.MethodsA total of 18,131 individual match observations were collected from outfield players competing during the 2018/2019 and 2019/20 seasons in the First and Second Spanish Professional Soccer Leagues (LaLiga™). High Metabolic Load Distance (HMLD; distance covered with a power consumption above 25.5 W·kg−1 and accelerations or decelerations (e.g., accelerating from 2 to 4 m·s−2 for 1 s) were included), and HMLD per minute (HMLDmin) were analyzed by the ChryonHego® video-tracking system. Players were classified according to their playing position as follows: Central Backs (CB), Full Backs (FB), Center Midfields (CM), Wide Midfields (WM), and Forwards (FW).ResultsNo differences between competitive levels were found in any variable when all players were analyzed conjointly except for HMLDmin overall and during the second half. However, when playing positions were considered, differences between competitive levels were observed in all positions, mainly in HMLD and HMLD during the first-half variables. In addition, several differences between playing positions were observed, with CB presenting the lowest values in all variables compared to their counterparts in both competitive levels, whereas CM in First Division and WM in Second Division showed the highest values in the HMLD variables.DiscussionThe findings are of interest to analyze the HMLD in professional soccer players, enabling the adaptation and individualization of training in this population according to the competitive level and specific playing position of each player. creator: Tomás García-Calvo creator: José Carlos Ponce-Bordón creator: Eduard Pons creator: Roberto López del Campo creator: Ricardo Resta creator: Javier Raya-González uri: https://doi.org/10.7717/peerj.13318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 García-Calvo et al. title: Context dependent prediction in DNA sequence using neural networks link: https://peerj.com/articles/13666 last-modified: 2022-09-20 description: One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures. creator: Christian Grønbæk creator: Yuhu Liang creator: Desmond Elliott creator: Anders Krogh uri: https://doi.org/10.7717/peerj.13666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Grønbæk et al.