title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=644 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of nitrogen fertilizer on seed yield and quality of Kengyilia melanthera (Triticeae, Poaceae) link: https://peerj.com/articles/14101 last-modified: 2022-09-22 description: Widely distributed in the alpine sandy grassland in east Qinghai-Tibet Plateau (QTP), Kengyilia melanthera is considered as an ideal pioneer grass for the restoration of degraded and desertification grassland in the region. Under the special ecological and climatic conditions in the northwest Sichuan plateau located in east QTP, it is of great significance to optimize the amount of nitrogen fertilizer for the seed production of this species. The impact of nitrogen (N) fertilizer application on seed yield and quality of K. melanthera ‘Aba’, the only domesticated variety in the Kengyilia genus of Poaceae, was investigated based on two-year field experiments in the northwestern Sichuan plateau. The results showed that with the increase of N fertilizer application, the number of tillers, number of fertile tillers, 1,000-seed weight and seed yield of this species increased likewise. The optimum N fertilizer rate deduced in the present study was 180 kg·hm−2, where the number of fertile tillers 1,000-seed weight and seed yield reached the peak values. Interestingly, the standard germination rate, germination energy, accelerated aging germination rate, dehydrogenase and acid phosphatase activity of seeds were not affected by the increasing the input of N fertilizer. The comprehensive evaluation of membership function showed that the optimal N fertilizer treatment was 180 kg·hm−2 both for 2016 and 2017. This study provided a certain practical suggestion for the improvement of seed production of K. melanthera in the northwest Sichuan plateau. creator: Shuai Yuan creator: Yao Ling creator: Yi Xiong creator: Chenglin Zhang creator: Lina Sha creator: Minghong You creator: Xiong Lei creator: Shiqie Bai creator: Xiao Ma uri: https://doi.org/10.7717/peerj.14101 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yuan et al. title: Applying SARIMA, ETS, and hybrid models for prediction of tuberculosis incidence rate in Taiwan link: https://peerj.com/articles/13117 last-modified: 2022-09-21 description: BackgroundTuberculosis (TB) remained one of the world’s most deadly chronic communicable diseases. Future TB incidence prediction is a benefit for intervention options and resource-allocation planning. We aimed to develop rapid univariate prediction models for epidemics forecasting employment.MethodsThe surveillance data regarding Taiwan monthly TB incidence rates which from January 2005 to June 2017 were utilized for simulation modelling and from July 2017 to December 2020 for model validation. The modeling approaches including the Seasonal Autoregressive Integrated Moving Average (SARIMA), the Exponential Smoothing (ETS), and SARIMA-ETS hybrid algorithms were constructed and compared. The modeling performance of in-sample simulating training sets and pseudo-out-of-sample validating sets were evaluated by metrics of the root mean square error (RMSE), mean absolute percentage error (MAPE), mean absolute error (MAE), and mean absolute scaled error (MASE).ResultsA total of 191,526 TB cases with a highest incidence rate in 2005 (72.5 per 100,000 person-year) and lowest in 2020 (33.2 per 100,000 person-year), from January-2005 to December-2020 showed a seasonality and steadily declining trend in Taiwan. The monthly incidence rates data were utilized to formulate these forecasting models. Through stepwise screening and assessing of the accuracy metrics, the optimized SARIMA(3,0,0)(2,1,0)12, ETS(A,A,A) and SARIMA-ETS-hybrid models were respectively selected as the candidate models. Regarding the outcome assessment of model performance, the SARIMA-ETS-hybrid model outperformed the ARIMA and ETS in the short term prediction with metrics of RMSE, MAE MAPE, and MASE of 0.084%, 0.067%, 0.646%, and 0.870%, during the pseudo-out-of-sample forecasting period. After projecting ahead to the long term forecasting TB incidence rates, ETS model showed the best performance resulting as a 41.69% (range: 22.1–56.38%) reduction of TB epidemics in 2025 and a 54.48% (range: 33.7–68.7%) reduction in 2030 compared with the 2015 levels.ConclusionThis time series modeling might offer us a rapid surveillance tool for facilitating WHO’s future TB elimination milestone. Our proposed SARIMA-ETS or ETS model outperformed the SARIMA in predicting less or 12–30 months ahead of epidemics, and all models showed better in short or medium-term forecasting than long-term forecasting. creator: Mei-Mei Kuan uri: https://doi.org/10.7717/peerj.13117 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Kuan title: Antimicrobial resistance among Streptococcus equi subspecies zooepidemicus and Rhodococcus equi isolated from equine specimens submitted to a diagnostic laboratory in Kentucky, USA link: https://peerj.com/articles/13682 last-modified: 2022-09-21 description: BackgroundSurveillance of antimicrobial resistance (AMR) among veterinary pathogens is necessary to identify clinically relevant patterns of AMR and to inform antimicrobial use practices. Streptococcus equi subsp. zooepidemicus and Rhodococcus equi are bacterial pathogens of major clinical importance in horses and are frequently implicated in respiratory tract infections. The objectives of this study were to describe antimicrobial resistance patterns and identify predictors of AMR and multidrug resistance (MDR) (resistance to three or more antimicrobial classes) among equine S. zooepidemicus and R. equi isolates.MethodsAntimicrobial susceptibility data from equine specimens submitted to the University of Kentucky Veterinary Diagnostic Laboratory between 2012 and 2017 were used in the study. Temporal trends in AMR and MDR were assessed using the Cochran-Armitage test. Logistic regression was used to identify associations between patient characteristics and the following outcomes: (a) MDR among S. zooepidemicus isolates, and (b) resistance to macrolides and ansamycins (rifampin) among R. equi isolates. Logistic regression was also used to investigate whether resistance of S. zooepidemicus and R. equi isolates to an antimicrobial class could be predicted by resistance to other drug classes.ResultsThe vast majority of S. zooepidemicus (99.6%) and R. equi isolates (83%) were resistant to at least one antimicrobial agent, but no significant temporal trends in AMR were observed. Approximately half (53.3%) of the S. zooepidemicus isolates were multidrug-resistant, and there was a significant (p < 0.001) increasing temporal trend of MDR among S. zooepidemicus isolates. Resistance to penicillin, which is typically recommended for treatment of suspected S. zooepidemicus infections, also increased during the study period, from 3.3% to 9.5%. Among R. equi isolates, 19.2% were resistant to one or more macrolide antibiotics, 24% were resistant to rifampin, and 15.6% were resistant to both macrolide(s) and rifampin. For both organisms, resistance to an antimicrobial class could be predicted based on resistance profiles to other drug classes. For instance, significant (p < 0.01) predictors of β-lactam resistance among S. zooepidemicus isolates included resistance to macrolides (Odds Ratio (OR) = 14.7) and ansamycins (OR = 9.3). Resistance to phenicols (OR = 3.7) and ansamycins (OR = 19.9) were associated with higher odds of macrolide resistance among R. equi isolates.ConclusionsThe increase in MDR among S. zooepidemicus isolates is concerning. The observed levels of resistance to macrolides and rifampin among R. equi are also worrisome given the limited number of antimicrobials available for treatment of this organism. The findings of this study highlight the importance of ongoing surveillance of AMR to guide treatment decisions and directions for future research. creator: Jennifer Lord creator: Craig Carter creator: Jacqueline Smith creator: Stephan Locke creator: Erica Phillips creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.13682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lord et al. title: Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer link: https://peerj.com/articles/13774 last-modified: 2022-09-21 description: PurposeAltered DNA methylation, genetic alterations, and environmental factors are involved in tumorigenesis. As a tumor suppressor gene, abnormal EPHA5 methylation was found in gastric cancer (GC) tissues and was linked to the initiation, progression and prognosis of GC. In this study, the EPHA5 methylation level in peripheral blood leukocytes (PBLs) was detected to explore its relationship with GC risk and prognosis.MethodsA total of 366 GC cases and 374 controls were selected as the subjects of this study to collect their environmental factors, and the EPHA5 methylation status was detected through the methylation-sensitive high-resolution melting method. Logistic regression analysis was utilized to evaluate the associations among EPHA5 methylation, environmental factors and GC risk. Meanwhile, the propensity score (PS) was used to adjust the imbalance of some independent variables.ResultsAfter PS adjustment, EPHA5 Pm (positive methylation) was more likely to increase the GC risk than EPHA5 Nm (negative methylation) (ORb = 1.827, 95% CI [1.202–2.777], P = 0.005). EPHA5 Pm had a more significant association with GC risk in the elderly (ORa = 2.785, 95% CI [1.563–4.961], P = 0.001) and H. pylori-negative groups (ORa = 2.758, 95% CI [1.369–5.555], P = 0.005). Moreover, the combined effects of EPHA5 Pm and H. pylori infection (ORca = 3.543, 95% CI [2.233–5.621], P < 0.001), consumption of alcohol (ORca = 2.893, 95% CI [1.844–4.539], P < 0.001), and salty food intake (ORca = 4.018, 95% CI [2.538–6.362], P < 0.001) on increasing the GC risk were observed. In addition, no convincing association was found between EPHA5 Pm and the GC prognosis.ConclusionsEPHA5 methylation in PBLs and its combined effects with environmental risk factors are related to the GC risk. creator: Xu Han creator: Tianyu Liu creator: Jiabao Zhai creator: Chang Liu creator: Wanyu Wang creator: Chuang Nie creator: Qi Wang creator: Xiaojie Zhu creator: Haibo Zhou creator: Wenjing Tian uri: https://doi.org/10.7717/peerj.13774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Han et al. title: DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food link: https://peerj.com/articles/13788 last-modified: 2022-09-21 description: Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item. creator: Carol S. Henger creator: Emily Hargous creator: Christopher M. Nagy creator: Mark Weckel creator: Claudia Wultsch creator: Konstantinos Krampis creator: Neil Duncan creator: Linda Gormezano creator: Jason Munshi-South uri: https://doi.org/10.7717/peerj.13788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Henger et al. 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.