title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1286 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification, characterization and expression pattern analysis of APYRASE family members in response to abiotic and biotic stresses in wheat link: https://peerj.com/articles/7622 last-modified: 2019-09-11 description: APYRASEs, which directly regulate intra- and extra-cellular ATP homeostasis, play a pivotal role in the regulation of various stress adaptations in mammals, bacteria and plants. In the present study, we identified and characterized wheat APYRASE family members at the genomic level in wheat. The results identified a total of nine APY homologs with conserved ACR domains. The sequence alignments, phylogenetic relations and conserved motifs of wheat APYs were bioinformatically analyzed. Although they share highly conserved secondary and tertiary structures, the wheat APYs could be mainly categorized into three groups, according to phylogenetic and structural analysis. Additionally, these APYs exhibited similar expression patterns in the root and shoot, among which TaAPY3-1, TaAPY3-3 and TaAPY3-4 had the highest expression levels. The time-course expression patterns of the eight APYs in response to biotic and abiotic stress in the wheat seedlings were also investigated. TaAPY3-2, TaAPY3-3, TaAPY3-4 and TaAPY6 exhibited strong sensitivity to all kinds of stresses in the leaves. Some APYs showed specific expression responses, such as TaAPY6 to heavy metal stress, and TaAPY7 to heat and salt stress. These results suggest that the stress-inducible APYs could have potential roles in the regulation of environmental stress adaptations. Moreover, the catalytic activity of TaAPY3-1 was further analyzed in the in vitro system. The results showed that TaAPY3-1 protein exhibited high catalytic activity in the degradation of ATP and ADP, but with low activity in degradation of TTP and GTP. It also has an extensive range of temperature adaptability, but preferred relatively acidic pH conditions. In this study, the genome-wide identification and characterization of APYs in wheat were suggested to be useful for further genetic modifications in the generation of high-stress-tolerant wheat cultivars. creator: Wenbo Liu creator: Jun Ni creator: Faheem Afzal Shah creator: Kaiqin Ye creator: Hao Hu creator: Qiaojian Wang creator: Dongdong Wang creator: Yuanyuan Yao creator: Shengwei Huang creator: Jinyan Hou creator: Chenghong Liu creator: Lifang Wu uri: https://doi.org/10.7717/peerj.7622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Prevalence of generalized joint hypermobility, musculoskeletal injuries, and chronic musculoskeletal pain among American university students link: https://peerj.com/articles/7625 last-modified: 2019-09-11 description: The objective of this study was to investigate the prevalence of generalized joint hypermobility (GJH) in a university-aged population, whether young adults (aged 18–25 years) with GJH are prone to sustain more musculoskeletal injuries, and are more likely to suffer from chronic musculoskeletal pain. The study used an interactive survey to gather data; GJH was assessed using a cut-off Beighton score of ≥5 in accordance with the 2017 International Classification of EDS criteria. The analyzed sample consisted of 482 female and 172 male participants from Florida Gulf Coast University (USA). The prevalence of GJH in a university-aged population can be estimated at 12.5%. Women did not have higher rates of GJH than men. However, female participants showed significantly higher rates of hypermobility of the spine as well as the right knee and elbow joints. The Beighton scores did not differ by ethnicity/race. Female participants had a lower rate of self-reported injuries than male participants, although this difference was not significant. There was no difference in the proportion of all participants classified within different categories (0; 1–4; 5–9) of Beighton scores and whether or not they reported having been injured. Male and female participants reported chronic pain of joints and neck or back at the same rates across the Beighton score categories. Female participants, however, reported higher pain intensity for chronic neck and back pain. This study increases knowledge about a correlation between GJH, musculoskeletal injuries, and chronic pain of joints, neck, and back in a university-aged population. creator: Peter R. Reuter creator: Kaylee R. Fichthorn uri: https://doi.org/10.7717/peerj.7625 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Reuter and Fichthorn title: Propagule pressure does not consistently predict the outcomes of exotic bird introductions link: https://peerj.com/articles/7637 last-modified: 2019-09-11 description: Some have argued that the role of propagule pressure in explaining the outcomes of bird introductions is well-supported by the historical record. Here, we show that the data from a large published database (including 832 records with propagule information) do not support the conclusion that propagule pressure is the primary determinant of introduction success in birds. A few compendia of historical reports have been widely used to evaluate introduction success, typically by combining data from numerous species and introduction locations. Very few taxa, other than birds, have usable spatially explicit records of introductions over time. This availability of data inflates the perceived importance of bird analyses for addressing factors related to invasion success. The available data allow limited testing of taxonomic and site-level factors of introduction outcomes. We did find significant differences in effort and success probabilities among avian orders and across highly aggregated spatial regions. As a test of a standard and logical expectation of the propagule pressure hypothesis, we concentrated on introductions with the smallest propagules, because it is for these the hypothesis is most likely to be correct. We analyzed the effect of numbers released in small propagules (two through 10) for 227 releases. Weighted linear regression indicated no significant effect of propagule size for this range of release size. In fact, the mean success rate of 28% for propagules of 2–10 isn’t significantly different than that of 34% for propagules of 11–100. Following the example of previous analyses, we expanded the statistical test of propagule pressure to include the full range of release numbers. No significant support for the propagule pressure hypothesis was found using logistic regression with either logit or complementary log-log link functions. creator: Michael P. Moulton creator: Wendell P. Cropper uri: https://doi.org/10.7717/peerj.7637 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Moulton and Cropper title: Genetic associations of vitamin D receptor polymorphisms with advanced liver fibrosis and response to pegylated interferon-based therapy in chronic hepatitis C link: https://peerj.com/articles/7666 last-modified: 2019-09-11 description: Vitamin D receptor (VDR) modulates host immune responses to infections such as hepatitis C virus (HCV) infection, including interferon signaling. This study aimed to investigate the associations of VDR polymorphisms with advanced liver fibrosis and response to pegylated interferon (PEG-IFN)-based therapy in patients with chronic HCV infection. In total, 554 Thai patients with chronic HCV infection treated with a PEG-IFN-based regimen were enrolled. Six single-nucleotide polymorphisms (SNPs) were genotyped: the IL28B C > T (rs12979860) SNP and five VDR SNPs, comprising FokI T > C (rs2228570), BsmI C > T (rs1544410), Tru9I G > A (rs757343), ApaI C > A (rs7975232), and TaqI A > G (rs731236). In total, 334 patients (60.3%) achieved sustained virological response (SVR), and 255 patients (46%) were infected with HCV genotype 1. The bAt (CCA) haplotype, consisting of the BsmI rs1544410 C, ApaI rs7975232 C, and TaqI rs731236 A alleles, was associated with poor response (in terms of lack of an SVR) to PEG-IFN-based therapy. The IL28B rs12979860 CT/TT genotypes (OR = 3.44, 95% CI [2.12–5.58], p < 0.001), bAt haplotype (OR = 2.02, 95% CI [1.04–3.91], p = 0.03), pre-treatment serum HCV RNA (logIU/mL; OR = 1.73, 95% CI [1.31–2.28], p < 0.001), advanced liver fibrosis (OR = 1.68, 95% CI [1.10–2.58], p = 0.02), and HCV genotype 1 (OR = 1.59, 95% CI [1.07–2.37], p = 0.02) independently predicted poor response. Patients with the bAt haplotype were more likely to have poor response compared to patients with other haplotypes (41.4% vs 21.9%, p = 0.03). The FokI rs2228570 TT/TC genotypes (OR = 1.63, 95% CI [1.06–2.51], p = 0.03) and age ≥55 years (OR = 2.25; 95% CI [1.54–3.32], p < 0.001) were independently associated with advanced liver fibrosis, assessed based on FIB-4 score >3.25. VDR polymorphisms were not associated with pre-treatment serum HCV RNA. In Thai patients with chronic HCV infection, the bAt haplotype is associated with poor response to PEG-IFN-based therapy, and the FokI rs2228570 TT/TC genotypes are risk factors for advanced liver fibrosis. creator: Kessarin Thanapirom creator: Sirinporn Suksawatamnuay creator: Wattana Sukeepaisarnjaroen creator: Pisit Tangkijvanich creator: Panarat Thaimai creator: Rujipat Wasitthankasem creator: Yong Poovorawan creator: Piyawat Komolmit uri: https://doi.org/10.7717/peerj.7666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thanapirom et al. title: Risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia: a case–control study in a Pakistani cohort link: https://peerj.com/articles/7195 last-modified: 2019-09-10 description: AIMSB-cell acute lymphoblastic leukemia (B-ALL) is amongst the most prevalent cancers of children in Pakistan. Genetic variations in FLT3 are associated with auto-phosphorylation of kinase domain that leads to increased proliferation of blast cells. Paired box family of transcription factor (PAX5) plays a critical role in commitment and differentiation of B-cells. Variations in PAX5 are associated with the risk of B-ALL. We aimed to analyze the association of FLT3 and PAX5 polymorphisms with B cell leukemia in Pakistani cohort.METHODSWe collected 155 B-ALL subject and 155 control blood samples. For analysis, genotyping was done by tetra ARMS-PCR. SPSS was used to check the association of demographic factors of SNPs present in the population with the risk of B-ALL.RESULTSRisk allele frequency A at locus 13q12.2 (rs35958982, FLT3) was conspicuous and showed positive association (OR = 2.30, CI [1.20–4.50], P = 0.005) but genotype frequency (OR = 3.67, CI [0.75–18.10], P = 0.088) failed to show any association with the disease. At locus 9p13.2 (rs3780135, PAX5), the risk allele frequency was significantly higher in B-ALL subjects than ancestral allele frequency (OR = 2.17, CI [1.37–3.43], P = 0.000). Genotype frequency analysis of rs3780135 polymorphism exhibited the protective effect (OR = 0.55, CI [0.72–1.83], P = 0.029). At locus 13q12.2 (rs12430881, FLT3), the minor allele frequency G (OR = 1.15, CI [1.37–3.43], P = 0.043) and genotype frequency (OR = 2.52, P = 0.006) reached significance as showed p < 0.05.CONCLUSIONIn the present study, a strong risk of B-cell acute lymphoblastic leukemia was associated with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect. Additionally, other demographic factors like family history, smoking and consanguinity were also found to be important in risk assessment. We anticipate that the information from genetic variations in this study can aid in therapeutic approach in the future. creator: Ammara Khalid creator: Sara Aslam creator: Mehboob Ahmed creator: Shahida Hasnain creator: Aimen Aslam uri: https://doi.org/10.7717/peerj.7195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Khalid et al. title: Abundance of arthropods as food for meadow bird chicks in response to short- and long-term soil wetting in Dutch dairy grasslands link: https://peerj.com/articles/7401 last-modified: 2019-09-10 description: BackgroundThroughout the world, intensive dairy farming has resulted in grasslands almost devoid of arthropods and birds. Meadow birds appear to be especially vulnerable during the chick-rearing period. So far, studies have focused mainly on describing population declines, but solutions to effectively stop these trends on the short-term are lacking. In this study at a single farm, we experimentally manipulated soil moisture through occasional irrigation, to mitigate against early season drainage and create favorable conditions for the emergence of above-ground arthropods during the meadow bird chick rearing phase.MethodsTo guarantee the presence of at least a sizeable arthropod community for the measurement of effects of wetting, we selected a farm with low intensity management. The land use and intensity of the study site and surroundings were categorized according to the national land use database and quantified using remote sensing imagery. From May 1 to June 18, 2017, we compared a control situation, with no water added, to two wetting treatments, a “short-term” (3 weeks) treatment based on wetting on warm days with a sprinkler system and a “long-term” treatment next to a water pond with a consistently raised water table from 2010. We measured soil temperature, soil moisture and resistance as well as the biomass of arthropods at 3-day intervals. Flying arthropods were sampled by sticky traps and crawling arthropods by pitfall traps. Individual arthropods were identified to Order and their length recorded, to assess their relevance to meadow bird chicks.ResultsThe land use analysis confirmed that the selected dairy farm had very low intensity management. This was different from most of the surrounding area (20 km radius), characterized by (very) high intensity land use. The experiments showed that irrigation contributed to cooler soils during midday, and that his happened already in the early part of the season; the differences with the control increased with time. In the short- and long-term treatments, soil moisture increased and soil resistance decreased from the mid-measurement period onward. Compared with the control, cumulative arthropod biomass was higher in the long-term treatment, but showed no change in the irrigation treatment. We conclude that small-scale interventions, such as occasional irrigation, favorably affected local soil properties. However, the effects on above-ground arthropod abundance currently appear limited or overridden by negative landscape-scale processes on arthropods. creator: Livia De Felici creator: Theunis Piersma creator: Ruth A. Howison uri: https://doi.org/10.7717/peerj.7401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 De Felici et al. title: lncRNA TMEM51-AS1 and RUSC1-AS1 function as ceRNAs for induction of laryngeal squamous cell carcinoma and prediction of prognosis link: https://peerj.com/articles/7456 last-modified: 2019-09-10 description: BackgroundLong non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with miRNAs to regulate target genes and promote cancer initiation and progression. The expression of lncRNAs and miRNAs can be epigenetically regulated. The goal of this study was to construct an lncRNA-miRNA-mRNA ceRNA network in laryngeal squamous cell carcinoma (LSCC) and reveal their methylation patterns, which was not investigated previously.MethodsMicroarray datasets available from the Gene Expression Omnibus database were used to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) between LSCC and controls, which were then overlapped with differentially methylated regions (DMRs). The ceRNA network was established by screening the interaction relationships between miRNAs and lncRNAs/mRNAs by corresponding databases. TCGA database was used to identify prognostic biomarkers.ResultsFive DELs (downregulated: TMEM51-AS1, SND1-IT1; upregulated: HCP5, RUSC1-AS1, LINC00324) and no DEMs were overlapped with the DMRs, but only a negative relationship occurred in the expression and methylation level of TMEM51-AS1. Five DELs could interact with 11 DEMs to regulate 242 DEGs, which was used to construct the ceRNA network, including TMEM51-AS1-miR-106b-SNX21/ TRAPPC10, LINC00324/RUSC1-AS1-miR-16-SPRY4/MICAL2/ SLC39A14, RUSC1-AS1-miR-10-SCG5 and RUSC1-AS1-miR-7-ZFP1 ceRNAs axes. Univariate Cox regression analysis showed RUSC1-AS1 and SNX21 were associated with overall survival (OS); LINC00324, miR-7 and ZFP1 correlated with recurrence-free survival (RFS); miR-16, miR-10, SCG5, SPRY4, MICAL2 and SLC39A14 were both OS and RFS-related. Furthermore, TRAPPC10 and SLC39A14 were identified as independent OS prognostic factors by multivariate Cox regression analysis.ConclusionDNA methylation-mediated TMEM51-AS1 and non-methylation-mediated RUSC1-AS1 may function as ceRNAs for induction of LSCC. They and their ceRNA axis genes (particularly TMEM51-AS1-miR-106b-TRAPPC10; RUSC1-AS1-miR-16-SLC39A14) may be potentially important prognostic biomarkers for LSCC. creator: Lian Hui creator: Jing Wang creator: Jialiang Zhang creator: Jin Long uri: https://doi.org/10.7717/peerj.7456 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hui et al. title: Wedge resection is equal to segmental resection for pulmonary typical carcinoid patients at localized stage: a population-based analysis link: https://peerj.com/articles/7519 last-modified: 2019-09-10 description: BackgroundMedical institutions worldwide have not reached a consensus on what surgery is the most advisable for pulmonary typical carcinoid (TC) patients at the localized stage. This research focuses on exploring whether wedge resection or segmental resection is the superior option.MethodsThe demographic and clinical information of 1,887 TC patients diagnosed at the localized stage from 2004 to 2015 was collected from the Surveillance, Epidemiology, and End Results (SEER) Program. Patient prognosis was evaluated by KM curves. The chi-square test was used to examine the variation between different groups that would be eliminated by propensity score matching (PSM). Univariate and multivariate Cox proportional hazard model analyses were used to evaluate prognostic values of relative factors.ResultsThe prognosis of TC was the most favorable for patients suffering from pulmonary squamous cell carcinoma (SCC), adenocarcinoma (ADC), and pulmonary carcinoids (PCs). The choice to have surgery, not the type of surgery chosen, was the most significant independent prognostic factor correlated with overall survival (OS) and lung cancer-special survival (LCSS). The prognostic result of the comparison between wedge resection and segmental resection was not statistically significant before or after PSM. In subgroup analysis, the inference still held. creator: Tao Yan creator: Kai Wang creator: Jichang Liu creator: Yukai Zeng creator: Fenglong Bie creator: Guanghui Wang creator: Jiajun Du uri: https://doi.org/10.7717/peerj.7519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Oceanographic habitat and the coral microbiomes of urban-impacted reefs link: https://peerj.com/articles/7552 last-modified: 2019-09-10 description: Coral reefs are in decline worldwide. In response to this habitat loss, there are efforts to grow, outplant, and restore corals in many regions. The physical oceanographic habitat of corals—such as sea temperature, waves, ocean currents, and available light—is spatially heterogeneous. We therefore hypothesize that outplant location may affect microbiomes, and ultimately, coral health and restoration success. We evaluated the influence of the physical oceanographic habitat on microbes in wild Porites astreoides and Siderastrea siderea. Tissue samples were collected at four Florida reefs in March, June, and September of 2015. We estimated oceanographic conditions from moored instruments, diver observations, remote sensing data, and numerical models. We analyzed microbiomes using amplicon 16S rRNA high-throughput sequencing data. We found microbial alpha-diversity negatively correlated with in situ sea temperature (which represented both the annual cycle and upwelling), as well as modeled alongshore currents, in situ sea-level, and modeled tide. Microbial beta-diversity correlated positively with significant wave height and alongshore currents from models, remotely-sensed relative turbidity, and in situ temperature. We found that archaea from the order Marine Group II decrease with increases in significant wave height, suggesting that this taxon may be influenced by waves. Also, during times of high wave activity, the relative abundance of bacteria from the order Flavobacteriales increases, which may be due to resuspension and cross-shelf transport of sediments. We also found that bacteria from the order SAR86 increase in relative abundance with increased temperature, which suggests that this taxon may play a role in the coral microbiome during periods of higher temperature. Overall, we find that physical oceanographic variability correlates with the structure of these coral microbiomes in ways that could be significant to coral health. creator: Stephanie M. Rosales creator: Christopher Sinigalliano creator: Maribeth Gidley creator: Paul R. Jones creator: Lewis J. Gramer uri: https://doi.org/10.7717/peerj.7552 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosales et al. title: Plant density and life history traits of Aconitum spicatum in North-central Nepal: effects of elevation and anthropogenic disturbances link: https://peerj.com/articles/7574 last-modified: 2019-09-10 description: Increasing cross-border trade of medicinal and aromatic plants (MAPs) has put heavy pressure on a considerable number of species in the Himalayas. One of the threatened species in Nepal is Aconitum spicatum. Unfortunately for this species and for many others, our knowledge on population ecology and performance across the distribution range is insufficient, hindering the formulation of species-specific management plans. We therefore studied density and population structure of A. spicatum and assessed variation in its life history traits among three populations (subalpine, lower alpine and alpine) along an elevation gradient (3,000–4,200 m a.s.l.) in Annapurna Conservation Area, north-central Nepal. The results show that human disturbances and topographic factors contributed to the variation in density and life history traits. The overall density ranged between 0.56 ± 0.09 (Mean ± SE) and 2.48 ±  0.24 plants/m2 with highest mean density in the lower alpine and lowest in the subalpine population. The subalpine population was also characterized by lower investment in reproductive structures with lowest seed mass and low seed viability and fecundity. Among the environmental variables tested, harvesting, animal droppings and fire appeared to be the most important factors affecting density of different life stages of A. spicatum. The prevailing harvesting pattern is destructive as it involves uprooting of the whole plant and this appears to be a main reason for low recruitment and reduced density of the subalpine population. The level of disturbance decreased with increasing elevation. In terms of reproductive effort, the alpine population performed best. Our results indicate that the viability of A. spicatum populations depends on controlling over-harvesting and pre-mature harvesting of tubers and protecting younger life stages from grazing, trampling and fire. We therefore recommend that when formulating management guidelines, measures aiming to mitigate such anthropogenic disturbances should be considered. creator: Deep J. Chapagain creator: Henrik Meilby creator: Suresh K. Ghimire uri: https://doi.org/10.7717/peerj.7574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chapagain et al.