title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1005 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot link: https://peerj.com/articles/10492 last-modified: 2020-12-08 description: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants. creator: Ahmed Khadr creator: Guang-Long Wang creator: Ya-Hui Wang creator: Rong-Rong Zhang creator: Xin-Rui Wang creator: Zhi-Sheng Xu creator: Yong-Sheng Tian creator: Ai-Sheng Xiong uri: https://doi.org/10.7717/peerj.10492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khadr et al. title: Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet link: https://peerj.com/articles/10496 last-modified: 2020-12-08 description: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and interspecific competition for food items is surmised to occur, predominantly within seagrass beds near the tidal inlet. However, this hypothesis needs to be tested in future studies. creator: Zeferino Blanco-Martínez creator: Roberto Pérez-Castañeda creator: Jesús Genaro Sánchez-Martínez creator: Flaviano Benavides-González creator: Jaime Luis Rábago-Castro creator: María de la Luz Vázquez-Sauceda creator: Lorena Garrido-Olvera uri: https://doi.org/10.7717/peerj.10496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Blanco-Martínez et al. title: Pro-inflammatory effect of obesity on rats with burn wounds link: https://peerj.com/articles/10499 last-modified: 2020-12-08 description: ObjectiveA burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study.Materials and methodsDifferent degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted.ResultsThe ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14.ConclusionBurn injury and obesity have a mutually synergistic effect on the body’s inflammatory response. creator: Chan Nie creator: Huiting Yu creator: Xue Wang creator: Xiahong Li creator: Zairong Wei creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.10499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nie et al. title: Self-reports vs. physical measures of spinal stiffness link: https://peerj.com/articles/9598 last-modified: 2020-12-07 description: BackgroundObjectively measured reduction in lumbar posterior-to-anterior (PA) stiffness is associated with pain relief in some, but not all persons with low back pain. Unfortunately, these measurements can be time consuming to perform. In comparison, the Lumbar Spine Instability Questionnaire (LSIQ) is intended to measure spinal instability and the Lumbar Spine Disability Index (LSDI) is created for self-reporting functional disability due to increased spinal stiffness. Given the above, the aim of this study is to compare measures of the LSIQ and LSDI with objective measures of lumbar PA stiffness as measured by a mechanical device, Vertetrack (VT), in patients with persistent non-specific low back pain (nsLBP).MethodsTwenty-nine patients with nsLBP completed the LSIQ and LSDI at baseline and after two weeks. On these same occasions, PA spinal stiffness was measured using the VT. Between measurements, patients received four sessions of spinal manipulation. The resulting data was analyzed to determine the correlation between the self-report and objective measures of stiffness at both time points. Further, the patients were categorized into responders and non-responders based on pre-established cut points depending on values from the VT and compared those to self-report measures in order to determine whether the LSIQ and the LSDI were sensitive to change.ResultsTwenty-nine participants completed the study. Measures from the LSIQ and LSDI correlated poorly with objectively measured lumbar PA stiffness at baseline and also with the change scores. The change in objectively measured lumbar PA stiffness following spinal manipulation did not differ between those who improved, and those who did not improve according to the pre-specified cut-points. Finally, a reduction in lumbar PA stiffness following intervention was not associated with improvement in LSIQ and LSDI outcomes.ConclusionsThe current data indicate that the LSIQ and LSDI questionnaires do not correlate with measures obtained objectively by VT. Our results suggest that these objective and self- reported measures represent different domains and as such, cannot stand in place of one another. creator: Jonas Nielsen creator: Casper Glissmann Nim creator: Søren O’Neill creator: Eleanor Boyle creator: Jan Hartvigsen creator: Gregory N. Kawchuk uri: https://doi.org/10.7717/peerj.9598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nielsen et al. title: Identification of key genes and pathways in endometriosis by integrated expression profiles analysis link: https://peerj.com/articles/10171 last-modified: 2020-12-07 description: The purpose of this study was to integrate the existing expression profile data on endometriosis (EM)-related tissues in order to identify the differentially expressed genes. In this study, three series of raw expression data were downloaded from GEO database. Differentially expressed genes (DEGs) in three tissue types were screened. GO, KEGG pathway enrichment analysis, core differential genes (CDGs) protein–protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA) were performed, finally, the dysregulation of Hippo pathway in ectopic endometrium (EC) was detected by Western blotting. A total of 1,811 DEGs between eutopic (EU) and normal endometrium (NE), 5,947 DEGs between EC and EU, and 3,192 DEGs between EC and NE datasets were identified. After screening, 394 CDGs were obtained, and 5 hub genes identified in the PPI network. CDGs enrichment and WGCNA network analysis revealed cell proliferation, differentiation, migration and other biological processes, Hippo and Wnt signaling pathways, and a variety of tumor-related pathways. Western blotting results showed that YAP/TAZ was upregulated, and MOB1, pMOB1, SAV1, LATS1 and LATS2 were downregulated in EC. Moreover, CDGs, especially the hub genes, are potential biomarkers and therapeutic targets. Finally, the Hippo pathway might play a key role in the development of endometriosis. creator: Ding Cui creator: Yang Liu creator: Junyan Ma creator: Kaiqing Lin creator: Kaihong Xu creator: Jun Lin uri: https://doi.org/10.7717/peerj.10171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cui et al. title: Influence of montane altitudinal ranges on species distribution models; evidence in Andean blow flies link: https://peerj.com/articles/10370 last-modified: 2020-12-07 description: BackgroundBlow flies are a family of dipterans of medical, veterinary and sanitary importance. We aim to predict the current geographical distribution of six neotropical blowfly species with different altitudinal ranges of distribution (high, medium, and lowlands) and degree of synanthropy (eusynanthropic, hemisynanthropic and asynanthropic) based on their existing fundamental niche (EA) in Northwestern South America.MethodsGeographical records were compiled based on data from museum specimens and literature. The accessible area hypothesis (M) was calculated based on three criteria: (1) Altitudinal range, (2) Synanthropy values deducted based on the Human Influence Index (HII) raster dataset, and (3). The mean dispersal capability of flies. The modeling was performed using the Maxent entropy modeling software. The selection of parameters was made with the R Program ENMeval package.ResultsThe models were assessed using the area under the operator-partial receiver curve (ROCp). The high statistical performance was evidenced in every modeling prediction. The modeling allowed identifying possible taxonomic inaccuracies and the lack of exhaustive collection in the field, especially for lowlands species. Geographical distribution predicted by the modeling and empirical data was remarkably coherent in montane species.DiscussionThe data obtained evidence that montane elevational ranges affect the performance of the distribution models. These models will allow a more precise predicting of medium and high elevation blow flies than lowlands species. Montane species modeling will accurately predict the fly occurrence to use such biological information for medical, legal, veterinary, and conservation purposes. creator: Mariano Altamiranda-Saavedra creator: Eduardo Amat creator: Luz Miryam Gómez-P uri: https://doi.org/10.7717/peerj.10370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Altamiranda-Saavedra et al. title: Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery link: https://peerj.com/articles/10381 last-modified: 2020-12-07 description: Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored. creator: Rohit Nandakumar creator: Valentin Dinu uri: https://doi.org/10.7717/peerj.10381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nandakumar and Dinu title: Trials in developing a nanoscale material for extravascular contrast-enhanced ultrasound targeting hepatocellular carcinoma link: https://peerj.com/articles/10403 last-modified: 2020-12-07 description: BackgroundMedical imaging is an important approach for the diagnosis of hepatocellular carcinoma (HCC), a common life threaten disease, however, the diagnostic efficiency is still not optimal. Developing a novel method to improve diagnosis is necessary. The aim of this project was to formulate a material that can combine with GPC3 of HCC for targeted enhanced ultrasound.MethodsA material of sulfur hexafluoride (SF6) filled liposome microbubbles and conjugated with synthesized peptide (LSPMbs) was prepared and assessed in vitro and vivo. Liposome microbubbles were made of DPPC, DPPG, DSPE-PEG2000,and SF6, using thin film method to form shell, followed filling SF6, and conjugating peptide. A carbodiimide method was used for covalent conjugation of peptide to LSMbs.ResultsThe prepared LSPMbs appeared round shaped, with size of 380.9 ±  176.5 nm, and Zeta potential of −51.4 ±  10.4mV. LSPMbs showed high affinity to Huh-7 cells in vitro, presented good enhanced ultrasound effects, did not show cytotoxicity, and did not exhibit targeted fluorescence and enhanced ultrasound in animal xenograft tumors.ConclusionExtravascular contrast-enhanced ultrasound targeted GPC3 on HCC may not be realized, and the reason may be that targeted contrast agents of microbubbles are hard to access and accumulate in the tumor stroma and matrix. creator: Size Wu creator: Xiyuan Lin uri: https://doi.org/10.7717/peerj.10403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu and Lin title: Neither ant dominance nor abundance explain ant-plant network structure in Mexican temperate forests link: https://peerj.com/articles/10435 last-modified: 2020-12-07 description: BackgroundAnt-plant mutualistic networks tend to have a nested structure that contributes to their stability, but the ecological factors that give rise to this structure are not fully understood. Here, we evaluate whether ant abundance and dominance hierarchy determine the structure of the ant-plant networks in two types of vegetation: oak and grassland, in two temperate environments of Mexico: Flor del Bosque State Park (FBSP) and La Malinche National Park (MNP). We predicted that dominant and abundant ant species make up the core, and submissives, the periphery of the network. We also expected a higher specialization level in the ant trophic level than in plant trophic level due to competition among the ant species for the plant-derived resources.MethodsThe ant-plant interaction network was obtained from the frequency of ant-plant interactions. We calculated a dominance hierarchy index for the ants using sampling with baits and evaluated their abundance using pitfall traps.ResultsIn MNP, the Formica spp. species complex formed the core of the network (in both the oak forest and the grassland), while in FBSP, the core species were Prenolepis imparis (oak forest) and Camponotus rubrithorax (grassland). Although these core species were dominant in their respective sites, they were not necessarily the most dominant ant species. Three of the four networks (oak forest and grassland in FBSP, and oak forest in MNP) were nested and had a higher number of plant species than ant species. Although greater specialization was observed in the ant trophic level in the two sites and vegetations, possibly due to competition with the more dominant ant species, this was not statistically significant. In three of these networks (grassland and oak forest of MNP and oak forest of FBSP), we found no correlation between the dominance hierarchy and abundance of the ant species and their position within the network. However, a positive correlation was found between the nestedness contribution value and ant dominance hierarchy in the grassland of the site FBSP, which could be due to the richer ant-plant network and higher dominance index of this community.ConclusionsOur evidence suggests that ant abundance and dominance hierarchy have little influence on network structure in temperate ecosystems, probably due to the species-poor ant-plant network and a dominance hierarchy formed only by the presence of dominant and submissive species with no intermediate dominant species between them (absence of gradient in hierarchy) in these ecosystems. creator: Brenda Juárez-Juárez creator: Mariana Cuautle creator: Citlalli Castillo-Guevara creator: Karla López-Vázquez creator: María Gómez-Ortigoza creator: María Gómez-Lazaga creator: Cecilia Díaz-Castelazo creator: Carlos Lara creator: Gibrán R. Pérez-Toledo creator: Miguel Reyes uri: https://doi.org/10.7717/peerj.10435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Juárez-Juárez et al. title: Association between parenting and non-suicidal self-injury among adolescents in Yunnan, China: a cross-sectional survey link: https://peerj.com/articles/10493 last-modified: 2020-12-07 description: BackgroundNon-suicidal self-injury (NSSI) among adolescents is prevalent and its rate has increased in recent years worldwide. Previous studies had investigated the association between parenting and childhood NSSI, but little is known about the relationship between parental rearing and repetition and severity of NSSI. The aim of this study was to investigate associations of parenting with NSSI and its repetition and severity in a representative adolescent sample from southwestern China.MethodsIn this cross-sectional study, a sample of 2,705 adolescents (F/M: 1,245/1,460; mean age: 13.4 ± 2.2 years) was recruited from 14 randomly selected schools in Lincang municipality, Yunnan province, China. A self-report questionnaire was used to collect data. The Adolescent Non-Suicidal Self-Injury Function Assessment Scale and the short Chinese Egna Minnen av Barndoms Uppfostran (s-EMBU-C) were used to evaluate NSSI behaviors and parenting style, respectively. Univariate and multivariate logistic regression models were adopted to examine association between parenting and NSSI.ResultsOverall lifetime prevalence of NSSI was 47.1% (95% CI [36.2–58.0]), with self-cutting being the most common form (23.5% (95% CI [19.3–27.7])), followed by hitting hard objects (23.4% (95% CI [20.2–26.7])) and pulling hairs (20.9% (95% CI [18.8–22.6])). In multiple logistic regression analyses, NSSI was positively associated with high level of father’s rejection (OR: 1.32 (95% CI [1.01–1.72])), high level of mother’s rejection (OR: 1.76 (95% CI [1.46–2.13])), low level of mother’s emotional warmth (OR: 1.42 (95% CI [1.15–1.75])), and high level of mother’s overprotection (OR: 1.74 (95% CI [1.49–2.03])), repeated NSSI was positively associated with low level of father’s emotional warmth (OR: 1.39 (95% CI [1.10–1.75])) and high level of mother’s overprotection (OR: 1.79 (95% CI [1.33–2.41])), and severe NSSI was positively associated with low level of father’s emotional warmth (OR: 1.64 (95% CI [1.11–2.43])) and high level of mother’s rejection (OR: 2.16 (95% CI [1.71–2.71])).ConclusionNSSI is common among adolescents in southwestern China. Negative parenting styles are associated with NSSI, repeated NSSI, and severe NSSI. The development of intervention measures for preventing or reducing NSSI among Chinese adolescents in school settings should consider parenting styles. creator: Yi Liu creator: Yuanyuan Xiao creator: Hailiang Ran creator: Xingting He creator: Linling Jiang creator: TianLan Wang creator: Run-xu Yang creator: Xiufeng Xu creator: Guangya Yang creator: Jin Lu uri: https://doi.org/10.7717/peerj.10493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu et al.